2010 Riparian/Fish Focus Team Report

San Francisco Bay Area
Upland Habitat Goals

Preserving Biological Diversity
for Future Generations
A Project of the Bay Area

Open Space Council
Riparian/Fish Focus Team Report

August 2010 Draft
Photo by E. Hoyer
Stuart B. Weiss, Ph.D., Nancy Schaefer and Ryan Branciforte
Project funded by:
California State Coastal Conservancy

Gordon and Betty Moore Foundation
California Coastal and Marine Initiative of the Resources Legacy Fund Foundation
Richard and Rhoda Goldman Fund
U.S. Fish and Wildlife Service Coastal Program at San Francisco Bay
RIPA RI AN/FISH FOCUS TEA M REPO RT AUGUST 2010 DRAFT
The San Francisco Ba y Area Upland Habitat Goals

(to be a chapter in the final report)
Table of Contents
PAGE
I. Introduction .............................................................................................................................................................3
II. Request of the Riparian/Fish Focus Team........................................................................................................................5
III. Riparian Defined..............................................................................................................................................................5
IV.Unique Role of Riparian Areas and Climate Change........................................................................................................5
V. Riparian and Fish Resources in the Bay Area...................................................................................................................6
VI. Riparian/Fish Focus Team Methodology.........................................................................................................................7
Working Assumptions and Guiding Principles................................................................................................................7
Selecting Conservation Targets........................................................................................................................................8
Compiling Available Data..............................................................................................................................................22
Anchor Watersheds and CalWater 2.2.1 Watersheds20
Setting Conservation Goals............................................................................................................................................23
Evaluating the Draft Conservation Lands Network for Meeting Riparian and Fish Conservation Goals.............27
CalWater 2.2.1 Planning Watersheds Gap Analysis Results..........................................................................30
VII. Viability of Fish and Stream Conservation Targets......................................................................................................40
Threats and Stresses for Coho Populations and Key Habitats.......................................................................................40
Assessing the Draft Conservation Lands Network for Riparian and Fish Viability......................................................46
VIII. Recommended Conservation Actions.........................................................................................................................53
IX. Data Gaps.....................................................................................................................................................................73
X. References.......................................................................................................................................................................74
Appendix A. Priority 1 and 2 Streams....................................................................................................a separate document

Appendix B. Essential Watersheds and Priority Stream Segments for Focused Conservation Actions
to Protect Native Fishes, San Francisco Estuary, California. Rob Leidy, U.S. EPA. ............................a separate document

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RIPARIAN/FISH FOCUS TEAM REPORT

I. Introduction
The Riparian/Fish Focus Team of the San Francisco Bay Area Upland Habitat Goals Project began
meeting in April 2008 and over the course of four meetings held through August 2008, crafted an
approach befitting the unique nature of riparian resources for establishing conservation goals. The
focus team included experts in stream geomorphology, hydrology and fish biology who actively shaped
the methodology for identifying conservation targets, setting conservation goals and recommending
conservation actions.
The report contains the following elements:
1. Identification of native fish species as conservation targets, using varied data sources and the
expert opinion of focus team members. Targets include anadromous and resident fish in streams
draining to the Estuary and directly to the coast.
2. Compilation of key hydrologic data sources including the National Hydrography Database (NHD)
and CalWater 2.2.1 watersheds.
3. Mapping of the spatial distribution of some target species and identifying key stream reaches and
watersheds that support them.
4. Prioritization of streams, stream reaches and watersheds according to importance to key fish
targets.
5. Gap analyses across watersheds, using current protected lands and a Draft Conservation Lands
Network, to map levels of land conservation in key watersheds.
6. Identification of general threats to viability of fish and riparian systems, using available documents
and expert opinion
7. Analysis of watershed integrity measures and viability threats across the study area, grouping
similar watersheds so that threats and conservation actions can be assessed at an appropriate scale.
8. Goals for riparian and fish conservation, aiming to conserve the integrity of the riparian network as
a whole as well as for specific fish targets.
9. Recommendations for conservation actions, including acquisition of fee and conservation
easements, restoration needs, and amelioration of watershed impacts.
10. Identification of data gaps.
The overarching goal of the Riparian/Fish Focus Team (RFFT) was to define a network of streams,
riparian habitat, associated upland areas, recommend conservation and stewardship actions that
conserve, restore and sustain riparian ecosystem functions to support healthy native fish populations.
The ecological processes of nearly all Bay Area riparian ecosystems have been disrupted, radically in
some cases, and as much as 95% of riparian habitat has been lost (CCMP 2007). To achieve effective
conservation of riparian ecosystems, the entire hydrologic continuum including low order headwater
catchments and high order streams must be considered for conservation and restoration. Restoration
focused only on in-channel fixes will not be successful without addressing problems throughout the
watershed including the basin, riparian corridor and floodplain areas. Similarly, protection and
restoration actions will not be successful in the long term absent appropriate stewardship.
The Upland Habitat Goals necessarily takes a regional approach over the thousands of miles of streams
in the Bay Area. Yet, the conservation and restoration needs of riparian systems are extremely site-
specific and cannot be accurately prescribed from this regional viewpoint. As a result, the
recommended conservation actions are general, focus on restoring ecological processes, and range
from comprehensive watershed planning to acquisition of headwaters areas to regulatory processes
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such as the designation of impaired waterways and the Total Maximum Daily Load (TMDL) planning
process. Two exceptions are the specific recommendations in the Public Draft Recovery Plan for
Central California Coast Coho ESU and Appendix B, Essential Watersheds and Priority Stream
Segments for Focused Conservation Actions to Protect Native Fishes, San Francisco Estuary,
California, prepared by Rob Leidy, Ph.D., US Environmental Protection Agency (Leidy 2008).
The Upland Habitat Goals Project used expert opinion and the best available data from multiple
sources to identify the priority streams, watersheds and riparian habitat for conservation actions. It
should be noted that while the project established priorities for streams, the importance of all riparian
corridors for biodiversity is acknowledged by the inclusion of all blue-line streams (1:24,000 National
Hydrography Dataset (NHD)) in the Conservation Lands Network. The resulting riparian conservation
network is embedded in and also extends beyond the Upland Habitat Goals study area boundaries into
the baylands, the subject of the San Francisco Baylands Ecosystem Goals. In the case of the Russian
and Pajaro River basins, one originates outside of the study area while the other flows outside of the
study area.
Conservation target viability was assessed using indicators of watershed ecological integrity, and was
conducted at the CalWater 2.2.1 planning watershed level, the finest scale readily available in GIS
format. Indicators used included human population density, impervious surfaces, cultivated
agriculture, timber harvesting, urbanization, distance to roads and protected lands (BPAD 2010).
These human activities impair the ecological processes by causing sedimentation, alteration of stream
channel geomorphology, loss of vegetation and fish passage barriers to name a few impacts.
Riparian/Fish Focus Team Members

Gordon Becker, Center for Ecosystem Management and Restoration
Kit Crump, National Oceanic and Atmospheric Administration
Rainer Hoenicke, San Francisco Estuary Institute
Leslie Ferguson, SF Bay Regional Water Quality Control Board
Jonathan Koehler, Napa County Resource Conservation District
Rob Leidy, US Environmental Protection Agency
Lisa Micheli, Sonoma Ecology Center
Paul Randall, EOA, Inc.
Ken Schwarz, Horizon Water and Environmental
Gail Seymour, California Department of Fish and Game
Phil Stevens, Urban Creeks Council
II. Role of the Riparian/Fish Focus Team
The Riparian/Fish Focus Team (RFFT) was asked to select fish and other relevant conservation targets,
describe species habitat requirements, establish conservation goals for the targets, identify a network of
streams with associated riparian and upland areas to accomplish the goals, and recommend
conservation actions. The focus team was also asked to identify processes and functions, and
recommend stewardship practices essential to the viability of the conservation targets. The
conservation targets and associated habitat requirements were then compared to the Draft Conservation
Lands Network developed by the Vegetation Focus Team for conservation of all vegetation types in the
study area. The Draft Conservation Lands Network was then adjusted to meet the goals set for riparian
and fish conservation targets. Because this focus team was asked to specifically address the needs of
fish, the members did not include the vital role of streams and riparian areas to numerous other species

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groups including birds, mammals, amphibians, reptiles and invertebrates. The fine filter focus teams
assigned to these species groups considered the habitat requirements of their conservation targets and
these were incorporated into the Conservation Lands Network when it was finalized.
III. Riparian Defined
The San Francisco Estuary Institute reviewed numerous definitions of riparian in Comparison of
Methods to Map California Riparian Areas (Collins et al. 2006). The most expansive definition,
adopted by the Riparian Habitat Joint Venture, is from the National Research Council and delineates
riparian areas as all lakeshores, stream or river channels, estuarine and marine shorelines, and wetland
margins. Definitions postulated by state and federal agencies are more typical in that they focus
primarily on streams and rivers and associated vegetation.
For the work of the Riparian/Fish Focus Team, Upland Habitat Goals chose the more limited definition
and focused on streams and rivers and associated riparian vegetation types. The Upland Habitat Goals
Coarse Filter Vegetation Map identifies three riparian vegetation types - Central Coast Riparian
Forests, Sycamore Alluvial Woodlands and Serpentine Riparian. All riparian vegetation types were
assigned a Rarity Rank 1 with a 90% conservation goal in all landscape units by the Vegetation Focus
Team during the coarse filter analysis. However, this goal is for existing vegetation as mapped and, as
noted above, much riparian vegetation has been lost. The need for extensive restoration of riparian
ecosystems is an important recommendation of the Upland Habitat Goals.
Acknowledging the validity of the Riparian Habitat Joint Venture definition, Upland Habitat Goals
includes marine shorelines in the Dune and Coastal Salt Marsh/Coastal Brackish Marsh vegetation
types. Both vegetation types are Rarity Rank 1 in all landscape units with a 90% conservation goal.
Furthermore, marine shorelines abut Cool Grasslands with a Rarity Rank 1 or 2 depending on the
landscape unit, and conservation goals of 90% and 75%, respectively. Freshwater wetlands are
represented by the Wet Meadows and Permanent Freshwater Marsh vegetation types, also Rarity Rank
1 in all the landscape units where they occur. Estuarine shorelines are included in the Baylands
Ecosystem Goals so are not covered here. Vernal pools were added as a Rarity Rank 1 conservation
target using Central Valley Vernal Pool Complexes (Holland).
IV. Unique Role of Riparian Areas in Climate Change Adaptation

Riparian areas are anticipated to play a unique role in climate change adaptation (Seavy et.al. 2009).
Riparian species tend to be particularly resilient because of adaptation to both seasonal and annual
variations in environmental conditions such as drought or flooding, both of which may increase in
frequency under climate change. The maintenance and restoration of riparian zones can enhance
resiliency both within and beyond riparian areas as the impacts of climate change continue to be felt.
Riparian habitats role as wildlife corridors for many plant and animal species offer species room to
move, further contributing to the significance of riparian areas to climate change adaptation. Rivers
and streams cross elevational gradients connecting different ecological zones, and aquatic with
terrestrial ecosystems. The cooler temperatures found in riparian zones can offer refuge as
temperatures increase. These attributes will make riparian areas an important component in climate
change adaptation.

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V. Riparian and Fish Resources in the San Francisco Bay Area

An extensive report titled Ecology, Assemblage Structure, Distribution and Status of Fishes in Streams
Tributary to the San Francisco Estuary, California, was completed in 2007 by Rob Leidy, Ph.D., U.S.
Environmental Protection Agency. Given the availability of this resource, only a brief overview is
offered here.
As with so many ecosystems in California, riparian and fish resources have been severely impacted by
human alterations to the landscape, destroying riparian forests and disrupting ecological processes.
Some estimates put the loss of riparian habitat as high as 95% (CCMP 2007). The federal listing of the
Evolutionarily Significant Unit (ESU) of Central California Coast coho salmon as an endangered
species and its extirpation from San Francisco Bay attest to these losses. Four Distinct Population
Segments (DPS) of steelhead coincide with the Upland Habitat Goals study area Central California
Coast, Central Valley, Northern California and South-Central California Coast and all four are listed
as threatened under the Endangered Species Act. Chinook salmon, primarily passing through the Bay,
are also threatened or endangered depending on the ESU.
In addition to anadromous species, there are eleven fish species endemic to the streams of San
Francisco Estuary (see Table 2) that are considered part of the Sacramento-San Joaquin Province
(Moyle, 2002). Of these eleven, the thicktail chub is extinct in Estuary watersheds, (Leidy, 2007).
Table 1 shows the geographic distribution and status of Estuary species.
Table 1. Current Geographic Distribution and Population Status of Stream Fishes of

the San Francisco Estuary (Leidy, 2007)

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Leidy also notes that Estuary streams typically support three to five of the following
assemblages as defined by the dominant fish in the assemblage.
1. Rainbow trout/upper mainstem-headwater tributary assemblage.
2. Mixed native fishes/middle mainstem-lower large tributary assemblage.
3. Mixed native-nonnative fishes/lower small to large mainstem assemblage.
4. Estuarine fishes/tidal riverine assemblage.
5. Reservoir-affected assemblage/lacustrine assemblage.
6. California roach/small, warm, intermittent tributary assemblage.
VI. Riparian/Fish Focus Team Methodology
Working Assumptions and Guiding Principles
The Riparian/Fish Focus Team adopted the Working Assumptions and Guiding Principles developed
by Robert Leidy, Ph.D., fisheries biologist with the U.S. Environmental Protection Agency, to guide
conservation target selection and final recommendations.
1. There is a strong correlation between watershed area and native fish species diversity. Therefore,
conservation actions focused on the largest watersheds have the potential to protect the greatest
number of native fish species. Similarly, there is a high correlation between San Francisco Estuary
anchor watersheds and essential streams for steelhead as identified in Becker et al. 2007 and the
diversity of other native fish species of conservation focus. All identified anchor watersheds and
essential streams for steelhead are included as priority watersheds for conservation actions for
other native fishes.
2. Anchor watersheds and essential streams identified in Becker et al. 2007 constitute the best
remaining habitat for steelhead and have the most immediate restoration needs and potential. But,
other streams in anchor and non-anchor watersheds that support steelhead and/or assemblages of
native fishes should be considered in establishing conservation goals.
3. Coho salmon are the rarest and most at risk species in the coastal areas. Streams and watersheds
that currently support or recently supported coho generally include the best remaining fish habitat,
especially for steelhead. Therefore, coho streams are considered the anchor watersheds and
essential streams for coastal areas.
4. Any prioritization of streams for fishes must consider the ecological importance of maintaining
lateral (riparian) and longitudinal connectively (tidal to headwaters) in streams. This is important
when considering buffer widths, fish immigration and emigration, and dispersal for re-colonization
and maintenance of populations.
5. Fishless streams, especially low order (i.e., first and second) headwaters, are critical to maintaining
native fishes, especially rainbow trout that may occur immediately downstream. The protection of
undeveloped headwaters of first and second order streams through easements and fee acquisition,
and other innovative mechanisms, is a conservation priority.
6. All freshwater dispersant fishes in estuary watersheds are variously isolated from other watersheds
depending on geographic location and other physical and biological factors. Within the estuary
there is a general geographic gradient of increasing watershed isolation from north to south and
from large to small drainage area. Therefore, whenever possible, conservation targets should be in
close proximity in order to decrease isolation.

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7. Several relatively small-to-medium sized watersheds support intact assemblages of native fishes.
Any conservation prioritization for native fishes must include a full range of watershed sizes.
8. Watersheds and stream segments from all landscape units should be represented in the
conservation strategy where possible and supported by the data.
9. Ecological redundancy of conservation targets is a priority. Goals should be set for a conservation
target in all landscape units within the targets geographic range.
10. All watershed segments dominated by wildland landscapes are a high priority as conservation
targets. Maintenance of existing land uses should be primarily through easements, fee acquisition,
and other novel management approaches. For example, the headwaters of Alameda Creek and
Coyote Creek watersheds are high priority for fish conservation targets, and actions should focus
on maintaining ranching land uses.
11. Streams flowing through urbanized baylands are important components to the ecological
functioning of less developed headwater landscapes, especially in terms of longitudinal
connectivity.
12. Recommended conservation actions for all stream segments flowing through landscapes
dominated by low-to-high density urban, residential, residential-commercial, and agricultural
landscapes, at a minimum, include (1) limiting additional streamside encroachment through the
establishment of appropriate riparian buffers, (2) maintaining the corridor for potential steelhead
restoration, and (3) the implementation of aggressive sediment and non-point source pollution
control measures.
Selecting Conservation Targets

Three main types of conservation targets riparian vegetation, fish species and streams were
selected by the Riparian/Fish Focus Team to advance the goal of fish biodiversity protection.
a. Riparian Vegetation Targets. The Vegetation Focus Team recognized the significance of
riparian vegetation to fish, birds and many other species groups. They also acknowledged the
dearth of accurate riparian vegetation maps covering the region and the gross underestimation of
the extent of riparian vegetation. The riparian vegetation that is mapped includes only the largest
remaining patches of at least four acres extent. Three riparian vegetation types were identified in
the Upland Habitat Goals Coarse Filter Vegetation Map Central Coast Riparian Forest,
Sycamore Alluvial Woodland and Serpentine Riparian. These vegetation types are Rarity Rank 1
with a corresponding conservation goal of 90% of the remaining vegetation in each landscape unit
where it occurs.
b. Fish Conservation Targets. The Riparian/Fish Focus Team selected all native fish species
found in the San Francisco Bay Area streams as conservation targets with the goal of maintaining
healthy assemblages of native fishes. Fish conservation targets are listed in Table 2.
The team opted to use the presence or absence of two listed anadromous fish - steelhead/rainbow
trout (0ncorhynchus mykiss) and coho salmon (Oncorhynchus kisutch) - and their
habitarequirements as surrogates indicating favorable conditions for native fishes. The
Evolutionarily Significant Unit (ESU) of Central California Coast coho salmon), extirpated from
estuary tributaries, was listed as threatened in 1997 and endangered in 2005 under the Endangered
Species Act. The Northern California, Central California and South-Central California Coast
Steelhead Distinct Population Segments (DPS) are still found in the estuary and coastal streams.

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All are federally listed as threatened. Recovery plans have not been started for these steelhead
DPS.
Table 2. Fish Conservation Targets

Native Native Resident Fish in
Native Resident Fish
Anadromous Fish Estuary*
Chinook Salmon California Roach** Arrow Goby
Chum Salmon Coastrange Sculpin Bay Goby
Coho Salmon Hardhead Delta Smelt
Pacific lamprey Hitch Jack Smelt
River lamprey Pacific Staghorn Sturgeon Longfin Smelt
Steelhead trout Prickly Sculpin Longjaw Mudsucker
Riffle Sculpin Northern Anchovy
Rainbow trout Pacific Herring
Sacramento blackfish Speckled Sandab
Sacramento Perch Starry Flounder
Sacramento pikeminnow Tidewater goby
Sacramento splittail
Sacramento sucker
Shiner Perch
Thicktail Chub
Three-spine Stickleback
Tule perch
White Sturgeon
*Typical range is in the estuary, a separate class where importance of Upland Habitat Goals is to the
health and integrity of watersheds entering the Bay and ocean.
**Endemic fishes of the Sacramento-San Joaquin Province known from streams of the San Francisco
Estuary (Leidy 2007) in bold.
The streams that currently support coho and steelhead are the most intact watersheds that
supply the complex habitat needs of anadromous fish, as well as the habitat requirements of
the other native fishes. Small runs of chinook and chum salmon are present in some streams,
but quick examination of their overlapping distributions with coho and steelhead indicate that
their habitat requirements are well-represented by those for coho and steelhead. However,
there are valuable and unique assemblages of other native fishes, as well as land-locked
rainbow trout whose habitat requirements are not sufficiently covered by steelhead and these
areas were added as conservation targets based on the expert opinion of focus team members.
Jonathan Koehler with the Napa River Resource Conservation District compiled data on the
fishes of the Napa River watershed and created the graphic in Figure 1. The figure illustrates
the range for native fish using channel slope classification and captures the importance of
protecting and restoring streams throughout their lengths. Focus team members
acknowledged the applicability of the channel slope classification because the Napa River
Basin supports (or has supported) nearly all of the native fish taxa of the region, and has the
range of habitats found throughout the watersheds draining to the Bay.

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Figure 1. Napa River Basin Fish Community (Koehler, 2007)
c. Stream Conservation Targets. As noted previously, the Riparian/Fish Focus Team

chose all Bay Area streams as conservation targets. They also chose to divide the streams into
three priorities to indicate relative importance. Priority rankings do not increase or decrease
conservation goals but focus attention on the most important streams and watersheds,
especially for listed anadromous fish and important assemblages of native fishes. The
prioritization is a guide for restoration efforts. It should be noted that some stream priority
rankings may change if California red-legged frog, Foothill yellow-legged frog and Western
pond turtle are present which will be determined by the Amphibians, Reptiles and
Invertebrates Focus Team.
Within the San Francisco Estuary, two primary data sources were used to identify priority
streams. The first is the San Francisco Estuary Watersheds Evaluation: Identifying
Promising Locations for Steelhead Restoration in Tributaries of the San Francisco Estuary
report, completed by the Center for Ecosystem Management and Restoration (CEMAR) in
August 2007 (Becker et al. 2007) which was used to identify priority steelhead streams. The
second source for estuary tributaries is Appendix B Essential Watersheds and Priority Stream
Segments for Focused Conservation Actions to Protect Native Fishes, San Francisco Estuary,
California, drafted by Rob Leidy, Ph.D., US Environmental Protection Agency (Leidy 2008)
and edited by the focus team. This document represents a significant compilation of expert

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knowledge for Bay Area streams broken down by stream segments and offers detailed
information on species presence and stream conditions.
The Becker et al. 2007 report identified tributaries to the San Francisco Estuary with the
highest probability of restoring of steelhead populations if protected and restored. The
authors screened the 58 Bay Area watersheds tributary to the estuary using two criteria. The
first criterion was the presence of reproducing steelhead populations and the second was the
amount of available rearing habitat. The underlying assumption is that watersheds with the
greatest amount of functioning steelhead rearing habitat are most likely to contribute to smolt
production which in turn strengthens the regional spawning run. Rearing habitat was broken
down into suitable and available categories. Suitable habitat refers to areas that can support
juvenile rearing without regard to the presence of passage barriers. Available habitat refers to
areas that are accessible to spawning steelhead and can support juvenile rearing, including
stream reaches above barriers that have a good probability of removal.
With available rearing habitat identified, and upon additional analysis, the authors concluded
that 8 of the regions watersheds account for roughly 75% of the regional steelhead rearing
habitat. These watersheds with the most extensive habitat were deemed Anchor Watersheds
as an indication of their significance. Anchor watersheds are Alameda, Coyote, San
Francisquito, Corte Madera, Sonoma and Suisun creeks and the Guadalupe and Napa rivers.
Further analysis of 54 streams within these watersheds identified 43 essential streams, listed
in Table 3, accounting for the majority of available rearing habitat (approximately 83%)
where restoration efforts should be focused. Map 1 shows the anchor watersheds and
essential streams. The authors note that not all anchor watershed tributaries were included in
the analysis because the habitat in these tributaries had not been characterized precluding a
determination of the presence or absence of available steelhead rearing habitat. This omission
is recorded as a data gap.
The Leidy 2008 Report (Appendix B) provides more detail on the essential streams and
includes additional streams and stream segments important to native fishes.

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Table 3. Anchor Watersheds and Essential Streams of the San Francisco Estuary
(Becker et al. 2007)
CEMAR Anchor CEMAR Anchor

Watersheds/ CEMAR Watersheds/ CEMAR
CalWater 2.2.1 Essential Streams CalWater 2.2.1. Essential Streams
Hydrologic Area Hydrologic Area
San Francisquito
Alameda Creek/
Alameda Creek Creek/ portion of Palo Bear Creek
Alameda HA
Alto HA
Indian Joe Creek Los Trancos Creek
San Antonio Creek McGarvey Gulch
Stonybrook Creek San Francisquito Creek
Corte Madera Creek/ Squeler Gulch/Purisima
Cascade Creek
San Rafael HA Creek
Corte Madera Creek West Union Creek
Sonoma Creek/
San Anselmo Creek Bear Creek
Sonoma Creek HA
Coyote Creek/
Arroyo Aguague Calabazas Creek
Coyote HA
Coyote Creek Carriger Creek
Upper Penitencia
Fowler Creek
Creek
Guadalupe River/
Alviso Slough Redwood Creek
Guadalupe HA
Arroyo Calero Sonoma Creek
Guadalupe Creek Trinity Creek
Suisun Creek/
Guadalupe River Suisun Creek
portion of Fairfield HA
Pheasant Creek
Napa River/
Campbell Creek
Napa River HA
Carneros Creek
Dry Creek
Heath Canyon Creek
Iron Mine Creek
Montgomery Creek
Napa Creek
Napa River
Pickle Canyon Creek
Redwood Creek
Ritchey Creek
Segassia Canyon
Creek
Sulphur Creek
Wing Canyon Creek

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Map 1. Anchor Watersheds and Essential Streams of the San Francisco Estuary
(Becker et al. 2007)

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For coastal streams, the primary data source used to identify streams and relative priority was the
Public Draft Recovery Plan for the ESU of the CCC Coho Salmon. Some steelhead streams
contributing to coho streams were also added from the CalFish Steelhead winter distribution
dataset.
Table 4 lists the watersheds and streams from the Public Draft Recovery Plan for the ESU of
California Central Coast Coho Salmon. Watersheds denoted with an I refers to their designation
as an Independent watershed. These are the large watersheds such as the Napa and Russian Rivers
that can persist on their own with little to no immigration from neighboring watersheds.
Map 2 illustrates Priority 1 and 2 stream conservation targets in the coastal areas.
Table 4. Watersheds from Public Draft Recovery Plan for the ESU of California
Central Coast Coho Salmon
Coho Watersheds Core Area Streams Coho Watersheds Core Area Streams
Gazos Creek Gazos Creek Salmon Creek Coleman Valley Creek
Old Womans Creek Finley Creek
Redwood Creek Redwood Creek Nolan Creek
Fern Creek Salmon Creek
Green Gulch Tannery Creek
Gualala River (I)* Pepperwood Creek Thurston Creek
Lagunitas Creek (I) Cheda Creek San Gregorio Creek Alpine Creek
Lower Lagunitas Bogess Creek
Creek floodplain and
estuarine areas
Olema Creek Harrington Creek
San Geronimo Mindego Creek
Pescadero Creek (I) No core areas San Gregorio
Pine Gulch No core areas Walker Creek Frink Canyon
Russian River (I) Devil Creek Walker Creek
Dutch Bill Creek
East Austin Creek
Felta Creek
Freezeout Creek
Green Valley Creek
Mill Creek
Palmer Creek
Purrington Creek
Sheephouse Creek
Upper East Gray Creek
Wallace Creek
*indicates an Independent stream

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Map 2. Priority 1 and 2 Coastal Streams

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Using these data sources along with additional datasets detailed in the next section, the following
priority classifications were established for streams. Map 3 displays Priority 1, 2 and 3 streams.
Table 5 lists the number of native fish, endemic species and presence of coho and steelhead for
Estuary watersheds. Appendix A is a list of all Priority 1 and 2 streams.
Priority 1 Streams
These are streams and watersheds with existing steelhead populations, available rearing habitat
and historic or current coho populations that must be conserved and/or restored as soon as possible
for fish conservation to be effective.
The following criteria were used to identify Priority 1 streams.

1. The essential streams for steelhead draining to the San Francisco Estuary as identified in the
Becker et.al Report.
2. Streams identified as Core Areas in the Public Draft Recovery Plan for the Evolutionarily
Significant Unit of Central California Coast Coho Salmon. Both Dependent and Independent
coho streams were given a Priority 1.
3. Streams with high diversity assemblages of warm-water native fish in streams draining to the
Bay (Leidy 2008 Report).
4. The healthiest steelhead streams in the Pajaro River Basin (expert opinion of RFFT and Santa
Clara County HCP).
5. Streams with reservoir dependent steelhead runs where steelhead are dependent on spawning
habitat below dams and adequate freshwater flows (Riparian/Fish Focus Team expert opinion)
including:
1) Alameda Creek tributaries below Calaveras and San Antonio Reservoirs

2) Coyote Creek below Anderson Reservoir
3) Dry Creek below Lake Sonoma
4) Lagunitas Creek below Kent Lake
5) Llagas Creek below Chesbro Reservoir
6) Russian River (Lake Mendocino, Eel River diversion)
7) San Lorenzo Creek below Lake Chabot
8) San Pablo Creek below San Pablo Reservoir
9) Stevens Creek below Stevens Creek Reservoir
10) Uvas Creek below Uvas Reservoir
Priority 2 Streams
Priority 2 streams and watersheds should receive substantial protection and restoration for long-
term fish conservation. Priority 2 streams have smaller steelhead, land-locked rainbow trout
populations and other/or healthy assemblages of native fish. They may also be isolated stream
segments with high conservation value. For example, Upper Stevens Creek in the Santa Cruz
Mountains North landscape unit supports resident rainbow trout, California roach and Sacramento
sucker; Coyote Creek above Coyote Reservoir supports rainbow trout and five other native fishes.
In coastal areas, all identified winter steelhead streams were included as Priority 2. These include
the majority of streams with any connection to the ocean. The following criteria were used to
identify Priority 2 streams:
1. Streams draining to San Francisco Estuary with less healthy steelhead runs (Becker et al. 2007
Report).

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2. Streams draining to San Francisco Estuary with assemblages of native fish other than
steelhead (Leidy 2008 Report).
3. Streams in the Pajaro River Basin with less healthy steelhead runs (Riparian/Fish Focus Team
expert opinion and Santa Clara Habitat Conservation Plan).
4. Coastal streams with steelhead draining into coho streams (including the Russian River basin)
(CalFish Winter Steelhead Distribution, Draft Coho Recovery Plan).
6. Best coastal steelhead streams not covered by coho salmon (CalFish Winter Steelhead
Distribution and Riparian/Fish Focus Team expert opinion).
7. Streams draining to the San Francisco Estuary with landlocked rainbow trout (Leidy 2008
Report).
8. Streams with reservoir anadromy where fish grow large in the reservoir and run upstream to
spawn. Streams with such potential are listed below but note that there may be others not
listed in smaller reservoirs. These streams largely overlap with Priority 2 streams other native
fish assemblages.
1) Calaveras Reservoir
2) San Antonio Reservoir
3) Lake del Valle
4) Anderson Reservoir
5) Coyote Reservoir
6) Lake Sonoma
7) Lake Hennessey
8) Chesbro Reservoir
9) Lake Chabot
10) San Pablo Reservoir
11) Stevens Creek Reservoir
12) Uvas Reservoir
Priority 3 Streams
All remaining streams are classified as Priority 3 because of the critical role played by all riparian
areas in providing hydrologic integrity, wildlife habitat, corridors, and buffering against climate
change.

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Map 3. Upland Habitat Goals Priority Streams

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DRAF T R I P A R I A N / F I S H F O C U S T E A M R E P O R T AUGUST 2010 DRAFT
Table 5. San Francisco Bay Watersheds Ranked by Presence of Native Species

(Robert Leidy, Ph.D., U.S. Environmental Protection Agency, 2008)
Number
Number Number O.
Estuary Watershed (County) special O. mykiss
Native Endemic mykiss
Anchor Watersheds in bold Italics status (A)
Species Species (LL)
species
Napa (Napa) 23 9 8 1 1
Petaluma (Sonoma) 19 7 7 1 0
Alameda (Alameda) 19 8 4 1 1
Coyote (Santa Clara) 19 6 5 1 1
Guadalupe 18 6 4 1 1
Walnut/San Ramon (Contra Costa) 14 7 5 1 1
Sonoma 15 5 4 1 1
Suisun (Solano) 13 7 3 1 1
Marsh 10 6 2 0 0
Green Valley 10 4 2 1 1
Corte Madera (Marin) 11 3 2 1 0
San Francisquito 9 3 2 1 1
Stevens 7 4 2 1 1
San Mateo (Sn Mateo) 7 3 2 1 1
San Lorenzo 7 3 2 1 0
Pinole 7 3 2 1 0
Novato 7 3 2 1 0
San Pablo 7 3 2 0 0
Arroyo San Jose 7 2 2 1 0
San Tomas Aquinas/Saratoga 6 3 2 1 0
Mt. Diablo 6 2 2 1 0
Arroyo Hambre 6 2 2 1 0
Rodeo 6 4 1 0 0
San Leandro 6 2 1 1 1
Arroyo Corte Madera del Presidio 6 2 2 1 0
Miller 6 2 2 1 0
Wildcat 5 2 1 1 1
Permanente 5 2 2 0 1
Matadero/Barron 5 3 1 0 0
Huichica 5 1 2 1 0
Adobe 5 2 1 0 0
American Canyon 5 2 1 0 0
Strawberry 4 2 1 0 0
Arroyo la Laguna 4 2 1 0 0
Codornices 4 0 1 1 0
Garrity 4 1 0 0 0
Schell 4 1 0 0 0
Sausal 3 0 1 0 1
Peralta 3 0 1 0 1
Lion/Horseshoe 3 0 1 0 1
Calabazas 3 1 1 0 0
Sulphur Springs 2 0 1 1 0
Cerrito 3 0 0 0 0
Refugio 2 0 0 0 0
Baxter 2 0 0 0 0
Temescal 2 0 0 0 0
Arroyo Viejo 2 0 0 0 0
Lower Penitencia 2 0 0 0 0
Redwood/Arroyo Ojo de Agua 2 0 0 0 0
Cordilleras 2 0 0 0 0
Laurel 2 0 0 0 0
Sanchez 2 0 0 0 0
Easton 2 0 0 0 0
Mills 2 0 0 0 0
Colma 2 0 0 0 0
Presidio (San Francisco) 2 0 0 0 0
Coyote Marin 2 0 0 0 0
Pacheco 2 0 0 0 0
Tolay 2 0 0 0 0
Glen Echo 1 0 0 0 0
Anchor Watersheds and CalWater 2.2.1. Watersheds
Upland Habitat Goals chose to use the most current edition of CalWater 2.2.1. for the analyses
rather than the Anchor Watersheds delineated in Becker et al. 2007. CalWater is the California
Statewide watershed delineation standard established by the California Interagency Watershed
Mapping Committee within the Natural Resources Conservation Service. CalWater was used
because it is a standardized dataset that allows for repeatable analyses and facilitates future
updates using the same methods. The coho recovery plan uses CalWater Planning Watersheds.
CalWater can be found at http://www.ca.nrcs.usda.gov/features/calwater/calwatershedsmap.html.
CalWater has several levels of watershed delineations. Most of the Upland Habitat Goals analyses
were conducted at CalWaters finest scale, the Planning Watershed (PWS), in addition to the
Hydrologic Area (HA) level.
In most cases, the CalWater 2.2.1 dataset allows ready comparison to the CEMAR Anchor
Watersheds and other datasets used to develop fish and riparian recommendations. However, the
Anchor Watersheds of the CEMAR report do not line up exactly with CalWater watershed levels
in all cases. Table 6 and Map 4 highlight the few areas of discrepancy.
Table 6. CEMAR vs. CalWater Watershed Levels
Calwater 2.2.1 Designation

CEMAR
CEMAR Anchor Watershed Watershed Hydrologic Hydrologic Super
Planning
Acreage Planning
Area Sub-Area Watershed
Watershed
Alameda
Alameda Creek 417,337
Creek
portion of San Anselmo
Corte Madera Creek 15,771
San Rafael & Ross Creek
Coyote
Coyote Creek 237,206
Creek
Guadalupe
Guadalupe River 102,161
River
Napa River 266,735 Napa River
portion of Portola
San Francisquito Creek 25,313
Palo Alto Valley
Sonoma
Sonoma Creek 99,080
Creek
portion of Suisun
Suisun Creek 32,600
Fairfield Creek

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Map 4. CEMAR vs. CalWater Watershed Levels

Page 21 of 76
Compiling Available Data

Poorly mapped riparian habitats represent a significant data gap. Riparian areas were identified
using the US Forest Service CalVeg GIS dataset that is remotely sensed from satellite imagery.
CalVeg has acknowledged spatial and classification accuracy issues, but is the only dataset
available for the entire study area. The San Francisco Estuary Institute has embarked on an
extensive riparian mapping effort that will provide more accurate data for future updates of the
Upland Habitat Goals.
To compensate for the absence of a comprehensive riparian vegetation layer, the National
Hydrography Dataset (NHD) 1:24,000 stream network (http://nhd.usgs.gov) was used as the base
coverage for riparian habitat. NHD captures the mainstems and major tributaries of all stream
systems in the region, and the database has ongoing quality control and improvements. The
1:24,000 scale of NHD does not capture numerous small headwater swales and seasonal streams,
the first and second order streams called out in Guiding Principle 5. However, these fine-scale
features are embedded within the Upland Habitat Goals Coarse Filter Vegetation Map and are
captured by the 100-hectare (250 acre) scale of the Marxan hexagons.
To illustrate this point, Figure 2 shows a series of CalWater 2.2.1 Planning Watersheds with the
NHD stream network, 100-hectare hexagonal planning units for Marxan, and hillshaded
topography in the Southern Mayacamas Mountains (the Upper Napa Valley is the flat area in the
upper right). The true first and second order headwater streams and swales are in the small
canyons radiating from the NHD streams, and greatly increase the length of the stream network.
Note how these upper watersheds are encompassed by the 100-hectare Marxan hexagons,
indicating that the Draft Conservation Lands Network captures these important hydrologic
features.
Figure 2. Inclusion of First and Second Order Streams in Upland Habitat Goals

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For fish conservation targets, available data was compiled on the ranges, occurrences and specific
priority watersheds. The key datasets used are the essential streams and anchor watersheds from the
Becker et al. 2007 and Leidy 2008 reports described above. Additional datasets used or reviewed are:
a. Salmonid Habitat Restoration Planning Resource for San Mateo and Santa Cruz Counties
compiled by Circuit Riders:
Historic Steelhead and Coho Streams
b. National Marine Fisheries Service:
Steelhead and Chinook distribution data
Steelhead and Chinook distribution data
Central California Coast Steelhead Critical Habitat and Distribution (PDF Map)
Public Draft Recovery Plan for the Evolutionarily Significant Unit of Central California Coast
Coho Salmon and pers comm. Kit Crump, NOAA.
c. CalFish:
Winter Steelhead Distributions, May 2007 - This dataset represents stream reaches that are
known or believed to be used by steelhead based on steelhead observations
Fish Barrier from the CA Statewide Passage Assessment Database (PAD).
Steelhead and Chinook Salmon Critical Habitat and distribution data
Chinook, Coho and Steelhead abundance data
Coho distribution data
d. National Oceanic and Atmospheric Administration
Critical Habitat Designations for West Coast Salmon and Steelhead (PDF Map)
e. Department of Fish and Game Coho Recovery Strategy
Present Distribution of Coho Salmon (PDF Map)
Setting Conservation Goals

Setting goals for riparian and fish conservation targets presented a challenge unique to these fine filter
targets due to the linear nature of the resource. The other fine filter focus teams reviewed coverage of
the Draft Conservation Lands Network for their species targets in each of the landscape units
established by the project (see Map 5). However, the landscape units were not a good fit for riparian
and fish resources so watersheds were the logical choice. The CalWater 2.2.1 Hydrologic Areas (see
Map 6) and Planning Watersheds were used for reviewing coverage by the Draft Conservation Lands
Network. Except where noted otherwise, the term Draft Conservation Lands Network includes lands
already protected and those proposed for conservation. Where listed, acreage goals refer to lands that
are not currently protected but are recommended for fee or easement acquisition, or long-term
cooperative agreement.
The Upland Habitat Goals did not include landscape units designated as urban (i.e., Santa Clara Urban)
when running the site selection software. The density of development, degraded, fragmented habitat
and incompatible land uses characteristic of these areas diminish species viability. However, as noted
in Guiding Principles 11 and 12, the linearity of streams and impacts to stream health from uses
throughout the watershed mandate the inclusion of streams throughout their length including urban
areas where many streams reach the Bay.
After selecting conservation targets and reviewing the available data, the focus team established goals
for each target category.
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Map 5. San Francisco Bay Area Landscape Units

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Map 6. CalWater 2.2.1 Hydrologic Areas
1. Riparian Vegetation. The Riparian/Fish Focus Team concurred with the Vegetation Focus
Team recommendation setting a 90% goal for all riparian vegetation types in all landscape units
where they occur. The acreage goals for each vegetation type in all landscape units where they
occur are shown in Table 7. The most abundant riparian vegetation type is the Central Coast
Riparian Forest (total acreage of 19,978) which therefore has the highest acreage conservation
goal at 12,117 acres (total acreage minus existing protected lands x 90% conservation goal). The
highest goals for Central Coast Riparian are found in the Mt. Hamilton, Russian River Valley,
Santa Cruz Mountains North and Sonoma Coast Range landscape units. Very little acreage
remains of Serpentine Riparian (167 acres) and Sycamore Alluvial Woodland (123 acres) which
have 86 and 37 acreage goals, respectively. As noted previously, riparian vegetation is poorly and
inconsistently mapped in the Bay Area and continues to be a significant data gap.
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Table 7. Acreage Goals for Riparian Vegetation Types by Landscape Unit

Protected
VEGETATION Rarity Total Unprotected Acreage Acreage
LANDSCAPE UNIT
TYPE Rank Acreage Acreage (BPAD Goals*
2008)
American Canyon 1 40 27 13 23
Blue Ridge Berryessa 1 237 223 14 200
Coastal Grasslands 1 1,172 1,000 173 882
Contra Costa Delta 1 93 82 12 72
Marin Coast Range 1 1,654 848 806 683
Middle East Bay Hills 1 110 49 61 38
Montezuma Hills 1 42 40 2 36
Mount Hamilton 1 2,027 1,209 818 1,006
Mt. Diablo Range 1 449 351 98 306
Napa Valley 1 992 920 72 821
North Contra Costa Valley 1 14 14 0 13
North East Bay Hills 1 246 157 89 132
Northern Mayacamas Mountains 1 32 32 0 29
Central Coast Point Reyes 1 1,025 111 914 9
Riparian Forests Russian River Valley 1 1,975 1,815 159 1,618
Santa Clara Valley 1 131 27 104 14
Santa Cruz Mountains North 1 3,257 2,207 1,049 1,882
Santa Rosa Plain 1 1,140 1,008 132 894
Sierra Azul 1 745 318 427 243
Solano Delta 1 159 137 22 121
Solano Plains 1 226 215 10 193
Sonoma Coast Range 1 1,515 1,242 274 1,090
Sonoma Mountains 1 538 447 91 393
Sonoma Valley 1 578 521 57 463
South East Bay Hills 1 383 243 140 205
Southern Mayacamas Mountains 1 422 393 29 351
Tri-Valley 1 249 148 101 123
Vaca Mountains West 1 329 312 17 279
Central Coast Riparian Forests Total 19,778 14,095 5,682 12,117
Mount Hamilton 1 104 52 52 41
Northern Mayacamas Mountains 1 17 17 0 15
Russian River Valley 1 13 13 0 12
Serpentine Riparian Santa Cruz Mountains North 1 8 4 4 4
Sierra Azul 1 15 8 8 6
Southern Mayacamas Mountains 1 4 4 0 3
Vaca Mountains West 1 5 5 0 4
Serpentine Riparian Total 167 103 64 86
Mount Hamilton 1 68 1 67 0
Sycamore Alluvial
North East Bay Hills 1 26 14 11 12
Woodland
Sierra Azul 1 29 28 0 26
Sycamore Alluvial Woodland Total 123 44 79 37
ACREAGE GOAL TOTALS 20,067 14,242 5,825 12,241
*Acreage goals are 90% of Total Acreage minus Protected Acreage. In other words, these are the areas yet to be
protected.
2. Native Fish. All thirty five native fish listed in Figure 1 were named as conservation targets
with a goal to restore healthy assemblages of native fish but the focus team stopped short of
setting population goals for fish in the Bay. Population goals were set for coho in the Public Draft
Recovery Plan for the ESU of CCC Coho Salmon released on March 18, 2010 states:

Page 26 of 76
The overarching goal of this Recovery Plan is to prevent the extinction of

wild CCC coho salmon and ensure their long term persistence in a viable,
self sustaining, and eventually harvestable status across the ESU.
Population targets for coho are listed below for the ten watersheds falling within the Upland
Habitat Goals study area.
Coho Recovery Target

Watershed
(adult salmon)
Gazos Creek 279

Gualala River 6,200
Lagunitas Creek 2,600
Pescadero Creek 2,300
Pine Gulch 252
Redwood Creek 272
Russian River 10,100
Salmon Creek n/a
San Gregorio Creek 1,363
Walker Creek 252
3. Streams. All streams are conservation targets with three priority levels. Appendix A is a full
list of all Priority 1 and 2 streams by watershed. Three overarching goals were articulated:
a. Protection of all streams via fee or easement acquisition, cooperative agreement or

protective policies.
b. Restoration of riparian habitat and ecosystem functions and processes once protection has
been secured.
c. Ensure sound stewardship practices on public and private lands to maintain the ecological
health of the streams.
The focus team emphasized the importance to healthy native fish populations of conserving
headwaters using fee purchase, conservation easements or other means of preventing disturbance
and development in these areas. Appendix B, Essential Watersheds and Priority Stream Segments
for Focused Conservation Actions to Protect Native Fishes, San Francisco Estuary, California by
Robert Leidy, Ph.D., US EPA, is a detailed listing of priority stream segments by watershed,
native fish species present, description of threats to viability and recommended conservation
actions for streams draining to the San Francisco Estuary.
Evaluating the Draft Conservation Lands Network for Meeting Riparian and
Fish Conservation Goals
Once the conservation goals were established, the focus team examined the Draft Conservation Lands
Network to evaluate coverage to meet these goals. Cartographic display, gap analyses and expert
review were employed for this evaluation.

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a. Cartographic Display. Map 6 displays the Draft Conservation Lands Network overlaid with
Priority 1 and 2 streams using dark and medium blue lines. Priority 3 streams, not shown on Map
6, are comprised of all remaining streams.
b. Gap Analysis. Using the Draft Conservation Lands Network, gap analyses using the CalWater
2.2.1 Planning Watersheds was completed. The gap analysis was used to identify Priority 1 and 2
stream watersheds not adequately covered by the Draft Conservation Lands Network so
adjustments could be made accordingly. A discussion of the gap analyses results follows.
c. Riparian/Fish Focus Team Review of Draft Map and Gap Analysis. Focus team
experts were asked to review the Draft Conservation Lands Network in Map 7 and the CalWater
2.2.1 Planning Watershed gap analysis results to evaluate coverage for fish and riparian habitat
goals and recommend adjustments if needed.

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Map 7. Conservation Lands Network with Stream Conservation Targets

Page 29 of 76
CalWater 2.2.1 Planning Watersheds Gap Analysis Results
In order to examine the levels of protection afforded by the current protected lands (BPAD 2010) and
the Draft Conservation Lands Network, a gap analysis employing the CalWater 2.2.1 Planning
Watersheds (PWS) was conducted. PWS can be directly tied to the priority levels for streams. The
gap analysis by Planning Watershed and stream priority answers the following questions:
1. What fraction of each Planning Watershed is currently protected?

2. What fraction is protected under the Draft Conservation Lands Network?
3. How do the protection levels change from current protected lands to Draft Conservation Lands
Network?
4. What is the geographic distribution of protection?
5. How do protection levels vary among Planning Watersheds supporting different priority streams?
The maps in Map 7 show current protection levels (BPAD 2010) on the left, and Draft Conservation
Lands Network protection levels on the right. Priority 1 and 2 streams are overlaid so that key
watershed areas can be quickly identified. It is immediately apparent that the Draft Conservation
Lands Network dramatically increases overall levels of watershed protection across the Bay Area, and
that the coverage of Priority 1 and 2 streams is greatly improved. For example, Hydrologic Areas such
as the Gualala River currently have little protection but the Draft Conservation Lands Network
captures many Planning Watersheds within the basin.
Note that the Draft Conservation Lands Network captured much of the headwaters areas, such as the
spine of the Mayacamas Mountains feeding the Napa River, Sonoma Creek and Russian River
tributaries.
While there are more than 500 PWS in the study area, the gap analysis was restricted to the Anchor
Watersheds draining to the Estuary and the coastal coho salmon watersheds identified in the Draft
Coho Recovery Plan. For each PWS nested in these larger areas, the percentages of currently
protected land (BPAD 2010), additional land under the Draft Conservation Land Network (CLN
Additions), Urban, Rural Residential (RR10), Cultivated Agriculture (Cultivated), and the unprotected
remaining undeveloped land (Remainder) were calculated. The stacked bar charts allow for rapid
assessment of current and proposed protection (combination of the green and blue bars, the total Draft
Conservation Land Network), the amount of available land, as well as the composition of the
developed land in the PWS.
The main purpose of this examination is to identify where protection levels fall short for key
watersheds. While it is not possible to always protect 100% of available lands within all PWS that
contain key fish targets, it is possible to set specific fine-filter targets by PWS, and/or add lands to the
Conservation Lands Network post-Marxan, if these adjustments are deemed necessary and adequately
justified.
A discussion of the gap analysis results follows for the Anchor and coho recovery plan watersheds,
highlighting particular PWS that have lower levels of protection under the Conservation Lands
Network. A detailed discussion of all PWS within all the larger watersheds is not feasible.

Page 30 of 76
Map 8. CalWater 2.2.1 Planning Watersheds Gap Analysis with Protected Lands (left) and Draft Conservation Lands Network
(right)
Note to focus team members: A high resolution pdf gap analysis map was included in the email
with this report so that one can zoom in and identify the location and spatial configuration of the
PWS and streams, as well as the land use composition of the watersheds. The PWS and stream
names can be seen when viewing the map at 200%.
The Napa and Sonoma Hydrologic Areas have been highlighted in Map 9 as a visual example; any
detailed examination should be done on the large map. The combination of the graphs and the large
map should provide the tools for systematic assessment of the Draft Conservation Lands Network with
regard to fish conservation targets.
Napa River Hydrologic Area
There are 23 PWS in the Napa Basin, all supporting Priority 1 and 2 streams. The mouth of the Napa
River has been excluded because much of it is Baylands and the city of Napa. Conservation Lands
Network protection ranges from 30% - 90%. Note the relatively high proportion of Cultivated land (up
to 25-35%), mainly vineyards. Remainder proportions range from 38% (Fir Canyon) to <5% (Conn
Creek, Garnett Creek, Lake Hennessey, and Moore Creek). Much of the CLN is in the headwaters of
the creeks along the crests of the Vaca Mountains and Southern Mayacamas (see Map 9).
Napa River HA
100%
90%
80%
70%
60%
50%
40% Remainder
30% Cultivated
20%
10% RR10
0% Urban
CLN Additions
Protected BPAD
Planning Watershed
Map 9. CalWater 2.2.1 Planning Watershed Gap Analysis for Sonoma and Napa
Hydrologic Areas

Page 33 of 76
Sonoma Creek Hydrologic Area
The Sonoma Creek HA consists of 9 PWS, all supporting Priority 1 and 2 streams. The CLN protects
from 10% (Harazthy) to 90% (Bear Creek). Substantial fractions of many of these PWS are in
Cultivated (mainly vineyards). The spatial arrangement of protected lands can be seen in Map 9; they
encompass much of the headwaters along the crest of Sonoma Mountain and much of the Southern
Mayacamas, with the exception of the Nathansen Creek PWS.
Sonoma Creek HA
100%
90%
80%
70%
60%
50%
40% Remainder
30% Cultivated
20%
RR10
10%
0% Urban
CLN Additions
Protected BPAD
Planning Watershed
Alameda Creek Hydrologic Area
The Alameda Creek HA is large, and the gap analysis is limited to Priority 1 (six PWS) and Priority 2
streams (thirty PWS). The Priority 1 PWS are the first set on the left and include the main stem of
Alameda Creek and tributaries that potentially support steelhead (once downstream barriers are
removed). Baby Peak and Valpe Creek are the least protected Priority 1 PWS under the Conservation
Lands Network (40% and 5%, respectively). Conservation Lands Network protection levels of Priority
2 PWS range from 8% (Coffee Mill Creek) to 100% in several PWS. Note that the least protected
PWS are in the remote backcountry of the watershed.
Alameda Creek HA
100%
90%
80%
70%
60%
50%
40%
30% Remainder
20%
10% Cultivated
0% RR10
Urban
CLN Additions
Protected BPAD
Planning Watershed

Page 34 of 76
Other Anchor Watersheds
The smaller Anchor Watersheds are presented in one graph, because the number of PWS in each is
limited. The Guadalupe River HA is well protected at present, with two urbanized PWS accounting
for most of the unprotected lands.
Coyote Creek HA has 5 PWS with Priority 1 streams. Penitencia Creek and Arroyo Aguague are well
protected by the Conservation Lands Network (80-100%). San Jose PWS has limited opportunities for
conservation because of intense urbanization (80% Urban). 40% of lower Coyote Creek (below
Anderson Reservoir) is Urban and Cultivated, and more than 50% is protected by the Conservation
Lands Network.
San Francisquito has a high proportion of RR10 in addition to Urban. Conservation Lands Network
protection levels on West Union Creek and Corte Madera Creek PWS are 55-60%, with little
Remainder.
In Corte Madera Creek in Marin, the two PWS supporting steelhead have almost all their available
land currently protected or added under the Conservation Lands Network.
In Suisun Creek, protection levels are lower (20-50%) than in the other Anchor Watersheds. Much of
the unprotected Remainder in Lake Curry is above the reservoir.
Other Anchor Watersheds

100%
90%
80%
70%
60%
50%
40%
30% Remainder
20%
10% Cultivated
0%
RR10
Urban
CLN Additions
Protected BPAD
Planning Watershed

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Lower Russian River
The Lower Russian River has five Core Area Coho watersheds, three of which are 100% protected by
the Conservation Lands Network, Green Valley-Rio Del is the most developed (50% in Urban,
Cultivated, and RR10), and is 30% protected by the Conservation Lands Network. Dutch Bill is the
least protected (45%). Conservation Lands Network protection among the seven Phase I watersheds
ranges from 20-85%. The four Phase II watersheds are the least protected (15-50%) on average.
Lower Russian River Coho

100%
90%
80%
70%
60%
50%
40%
30% Remainder
20%
10% Cultivated
0%
RR10
Urban
CLN Additions
Protected BPAD
Planning Watershed
Middle Russian River
There are three Core watersheds in the Middle Russian River. Wallace Creek is the least protected by
the Conservation Lands Network (20%). Of the fourteen Phase i watersheds, Dutcher Creek and
Redwood Log Creek are the most protected by the Conservation Lands Network (75%), and Lower
Dry Creek the least (although there is relatively little land available in Lower Dry Creek). Several of
the twenty four Phase II watersheds are completely protected by the Conservation Lands Network.
Middle Russian River Coho

100%
90%
80%
70%
60%
50%
40%
30% Remainder
20%
10% Cultivated
0%
RR10
Urban
CLN Additions
Protected BPAD
Planning Watershed

Page 36 of 76
Gualala River
The Gualala River spans both Sonoma and Mendocino Counties, only the Sonoma sections will be
considered here. Existing protected lands (BPAD 2010) are sparse. The one Gualala Core Area
watershed in Sonoma County, Pepperwood Creek, is protected at 50% by the Conservation Lands
Network. The six Phase I watersheds are all protected above 50%, with two at 90%. The least
protected of fifteen Phase II watersheds is Lower Rockpile Creek (22%), seven others are protected by
the Conservation Lands Network at 80% or more.
Gualala River Coho

100%
90%
80%
70%
60%
50%
40%
30%
Remainder
20%
10% Cultivated
0%
RR10
Urban
CLN Additions
Protected BPAD
Planning Watershed
Salmon Creek Marin
Salmon Creek has four Core watersheds, with one protected by the Conservation Lands Network at
>90% and the other three at 50-60%. Rural Residential is a significant component in Upper Salmon
Creek and Nolan Creeks.
Walker Creek is well protected by the Conservation Lands Network. In Lagunitas, only Nicasio Creek
has a large Remainder Fraction, much of this Remainder is above Nicasio Reservoir.
The three Bolinas coho watersheds are well protected by the Conservation Lands Network at 80-95%.
Salmon Creek - Marin Coho

100%
90%
80%
70%
60%
50%
40%
30% Remainder
20%
10% Cultivated
0%
RR10
Urban
CLN Additions
Protected BPAD
Planning Watershed

Page 37 of 76
San Mateo Coast
The San Gregorio Core watersheds are well protected by the Conservation Lands Network (80% and
90%, and the Phase I watersheds range from 50 to 80% protected by the Conservation Lands Network.
In Pescadero Creek, three Phase I watersheds are protected by the Conservation Lands Network at
>80%. Waterman Creek is the least protected, at 30%, and Honsinger is protected at 40%.
Gazos Creek, a Core coho watershed, is nearly entirely protected by the Conservation Lands Network.
San Mateo Coast Coho

100%
90%
80%
70%
60%
50%
40%
30% Remainder
20% Cultivated
10%
0% RR10
Urban
CLN Additions
Protected BPAD
Planning Watershed

Page 38 of 76
Map 10. Priority 1 and 2 Stream Miles by CalWater 2.2.1 Planning Watersheds
VII. Viability of Fish and Stream Conservation Targets

Assessing the viability of fish species and riverine habitats is immensely complex due to the
interaction of upstream and downstream land uses. Instream habitat conditions and native fish
populations are a function of conditions in the upper watersheds as well as floodplain areas making
restoration actions complex. Upper watersheds may consist of forest or rangeland while the lower
reaches of many Bay Area streams course through dense urban and/or cultivated agricultural areas
before reaching the Bay. Alameda Creek is a good example of the diverse vegetative cover and land
uses found along a streams length.
The Upland Habitat Goals Project adopted the approach used by National Marine Fisheries Service
{NMFS) and the California Department of Fish and Game (DFG) in the coho recovery planning
process to evaluate viability, threats and stresses because of its applicability to the native fish
conservation targets. Using a modified version of the Nature Conservancys Conservation Assessment
Planning, the recovery plan counts both key habitat and population as viability factors, also called
attributes that are measurable. Stresses are defined as the impacted condition of these attributes while
threats are the sources of the stresses. For example, poor agricultural practices (threat) can result in
erosion leading to sedimentation which is a stressor for several life stages of coho.
The Public Draft Recovery Plan for the Evolutionarily Significant Unit of Central California Coast
Coho Salmon was released on March 18, 2010. The recovery plan states that the primary threats to
coho are roads and railroads, droughts particularly from the Russian River south, and residential and
commercial development. Logging and wood harvesting are cited as a significant threat from the
Russian River north, and in some watersheds, channel modification or livestock farming and ranching
are significant threats. The full public draft plan is available for review at
http://swr.nmfs.noaa.gov/recovery/coho_recovery_plan_031810.htm.
Table 8 illustrates the viability approach employed by NMFS. For each coho life stage target, habitat
attributes and indicators are detailed. An overview of identified threats and corresponding stresses are
summarized below.
Threats and Stresses for Coho Populations and Key Habitats

1. Agricultural Practices. Agricultural practices are described as annual and perennial non-
timber crop farming and associated operations exclusive of grazing, ranching and timber harvest
operations. Such practices encompass all operations relating to developing, maintaining, plowing,
planting, harvesting, fertilizing, and irrigating row crops, orchards, vineyards, commercial
greenhouses, nurseries, gardens and similar land uses.
Stresses from agricultural practices are:
a. Water-borne pollutants such as sediment, pesticides and elevated nutrient levels.
b. Alteration in riparian vegetation integrity, diversity, function and composition.
c. Alteration of natural drainage channels and hydrology.
d. Channel simplification and alteration in streambank stability.
e. Cumulative, chronic and instantaneous water diversion and water withdrawal methods.
Table 8. Targeted Life Stage, Habitat Attributes and Indicators for Central California
Coast Evolutionarily Significant Unit of Coho Salmon. (Public Draft Recovery Plan for the
Evolutionarily Significant Unit of Central California Coast Coho Salmon, National Marine Fisheries Service,
March 2010)
2. Channel Modification. Certain actions can modify or degrade channel-forming processes and
stream morphology either directly or indirectly. Such actions include breaching or dredging of
estuarine lagoons, flood control, large wood debris removal, levee construction, vegetation
removal, herbicide applications, stream channelization and bank stabilization methods that
essentially channelize the stream.
Stresses from channel modification include:
a. Loss of instream and near stream habitat and habitat complexity.
b. Vegetation loss resulting in decreased channel roughness.
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c. Alteration of drainage channels and hydrology.

d. Alteration in riparian zone diversity, function and composition.
e. Alteration in channel and streambank stability.
f. Alteration or loss of floodplain, estuarine and wetland habitats.
g. Water-borne pollutants such as sediment, chemicals and adverse changes in nutrient levels.
h. Channel simplification, incision and floodplain disconnection.
3. Climate Change. The magnitude of climatic changes resulting from global warming is difficult
to predict. However, nearly all models predict weather events outside the normal range of
variation with increased air temperature being most probable. Changes in climate will result in
habitat shifting and alteration which will in turn lead to major changes in habitat composition and
location. Actions in response to a changing climate may include an increased demand for existing
water supplies and managing water storage to provide cool water refugia.
Stresses to be considered:
a. Changes in water temperature and natural hydrograph compared to salmonid migration
patterns.
b. Changes in vegetation communities that will adversely alter riparian process and function.
4. Fire and Fuel Management. Fighting wildfires as well as fire prevention actions, such as
prescribed burns, can be detrimental to coho habitat. The construction of fire breaks and roads,
use of fire retardants, fuels management activities, fire suppression and water use planning are
some of the detrimental actions associated with fire and fuel management.
Fire and fuel management stresses are:
a. Increased erosion, sedimentation and landslide potential.
b. Elevated fuel loading leading to catastrophic burns.
c. Loss of future large wood debris recruitment.
d. Alteration of vegetation and riparian communities from invasive species and post-fire
management.
5. Fishing and Collecting. The legal and illegal harvesting of salmonids can impact coho
viability. Actions include legal harvesting for recreation, subsistence, relocation, research and
collection and incidental capture. Illegal activities include poaching and unpermitted collection.
a. Mortality, injury and displacement.
b. Increased competition due to relocation.
c. Depensatory effects.
6. Hatcheries and Aquaculture. Hatchery and fish farming operations pose threats to viability
by inducing the stresses detailed below.
Stresses include:
a. Genetic (in- and outbreeding depression).
b. Intraspecific consequences to wild salmonids from escapes from fish farms (e.g., competition
for redd sites).
c. Parasites and diseases (e.g., bacterial kidney disease).
d. Pollution and elevated nutrients associated with facilities.
e. Introduction of out-of-Evolutionarily Significant Unit/Distinct Population Segment
salmonids.
f. Capture of wild spawners used to supplement hatchery program and thus reducing total run
size.
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g. Impediments to migration resulting from fish capture and rearing facilities.
7. Storms and Flooding. Storms and flooding become threats when exceeding average rainfall
amounts and exacerbating already degraded conditions.
a. Increases in frequency, duration and magnitude of flooding beyond natural conditions.
b. Flood fighting actions.
c. Loss of riparian and instream habitat attributes
d. Increased frequency of channel scour beyond natural conditions.
e. Increased turbidity beyond natural conditions.
8. Droughts. A drought can occur when there is less than average rainfall due to natural events or
human actions that result in impacts to streamflow and riparian conditions.
Stresses resulting from drought:
a. Insufficient flows to facilitate egg incubation, juvenile rearing, smolt outmigration and
juvenile upmigration.
b. Poor water quality leading to increased instream temperatures, low dissolved oxygen,
decreased food availability, increased concentrations of pollutants, etc.
c. Earlier than normal water diversion for anthropogenic purposes.
d. Insufficient flows to breach sandbars at river mouths.
9. Disease, Predation and Competition. Both native and non-native species can have
significant harmful impacts on salmonids and/or their habitat. Examples include sea lions,
mergansers and Arundo donax. Some specific actions contributing to this threat are the
introduction of non-native species that prey upon and/or compete with native salmonids; the
introduction of non-native vegetation that competes with and/or replaces native vegetation; and
the creation of conditions favorable to increased populations and/or concentrations of native
predators.
a. Habitat simplification.
b. Reduced feeding opportunities.
c. Shifts in native/non-native biotic communities and salmonid abundance resulting in
disproportional predation and competition.
d. Changes in water chemistry (e.g., eucalyptus, low dissolved oxygen resulting from increased
foreign biomass).
e. Impediments to instream movement and migration (Arundo donax).
10. Livestock farming and ranching. The grazing of livestock in one location or roaming a
larger area, if not managed carefully, can pose a threat to coho and other fish. Operations such as
feed lots, dairy farms, chicken farms and cattle ranching are included in this category.
a. Water-borne pollutants such as sediment, harmful chemicals, hormones and elevated nutrient
levels.
b. Alteration in riparian zone diversity, function and composition.
c. Alteration of drainage channels and hydrology due, in part, to soil compaction.
e. Water diversion and withdrawal.

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11. Logging and Wood Harvesting. Timber harvesting operations and post-logging impacts can
cause changes to the hydrograph, increased contribution of water-borne pollutants including
sediment and elevated nutrient levels. Timber harvesting requires the creation of skid trails,
landings and yarding corridors, re-opening old roads and/or the construction of new roads.
Maintaining the roads and the installation of erosion control structures results in further impacts.
Timberlands are also subject to land use conversion to vineyards or rural residential development
after harvesting.
Stresses resulting from timber harvest may include:
a. Water-borne pollutants such as sediment, harmful chemicals, and elevated nutrient levels.
b. Alteration in riparian zone integrity, diversity, function (i.e., large woody debris recruitment)
and composition.
e. Water diversion and withdrawal.
f. Compromised hillslope stability.
12. Mining. Mining and quarrying, such as instream gravel mining, cause numerous deleterious
impacts to streams and riparian habitat.
Stresses resulting from mining operations are:
a. Reduction in quantity and quality of stream gravel.
b. Reduced channel complexity.
c. Upstream channel changes such as headcuts.
d. Alteration in riparian zone integrity, diversity, function and composition.
e. Alteration in channel geometry and hydrology.
f. Alteration in streambank stability.
g. Water diversion and withdrawal.
h. Channel simplification, incision and disconnection from its floodplain.
i. Alterations/loss of floodplain/estuarine habitats.
j. Alterations in water quality from increased sedimentation, turbidity, elevated water
temperatures and inputs of toxic metals.
13. Recreational Areas and Associated Activities. Legal and illegal recreational activities can
alter, destroy and/or disturb habitats and species. These activities can include off road vehicle use,
motorboats, mountain bikes, trail maintenance, equestrian uses and golf courses.
a. Excessive erosion and sedimentation.
b. Stream fords and impacts from off road vehicle use in the streams.
c. Introduction of pollutants, garbage, toxic chemicals and changes in nutrient levels.
d. Alteration in riparian zone integrity, diversity, function and composition.
e. Alteration in streambank stability.
f. Channel simplification, incision and disconnection from its floodplain.
14. Residential and Commercial Development. Urban, industrial, suburban, recreational or

rural residential developments permanently alter the natural environment and encroach on
floodplains and riparian areas. Additional impacts result from household sewage, urban
wastewater, increased sedimentation, industrial effluents, garbage and solid waste.

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a. Introduction of pollutants, garbage, urban/industrial wastewater, sediment, toxic chemicals

and changes in nutrient levels.
b. Alteration in riparian zone integrity, diversity, function and composition.
c. Alteration in streambank stability.
d. Channel simplification, incision and disconnection from its floodplain.
e. Alteration of drainage channels and hydrology.
f. Increased stormwater runoff.
g. Water diversion and withdrawal.
h. Growth-inducing consequences.
15. Roads and Railroads. All manner of roads and railroads contribute to diminished stream
ecological health.
Stresses from roads and railroads include:
a. Chronic and acute introduction of sediment from surface erosion and drainage.
b. Fish passage impairment or blockage due to culverts, bridges, etc.
c. Risks of spills.
d. Alteration of drainage channels, hydrology, infiltration and runoff.
e. Alteration in riparian zone diversity, function and composition.
f. Channel simplification, incision and disconnection from its floodplain.
g. Alteration in channel and streambank stability.
h. Water-borne pollutants such as sediment, chemicals and adverse changes in nutrient levels.
i. Growth-inducing consequences.
16. Water Diversion and Impoundments. Appropriative and riparian surface water diversions,
groundwater pumping and the construction and maintenance of seasonal dams for water diversions
cause changes to water flow patterns outside the natural range of variation.
a. Chronic and acute introduction of sediment from surface erosion and drainage.
b. Fish passage impairment or blockage.
d. Alteration in riparian zone diversity, function and composition.
e. Alteration in channel and streambank stability.
f. Reduced freshwater inflow can contribute to alterations in and/or loss of floodplain and
estuarine habitats.
g. Water-borne pollutants such as sediment, chemicals and adverse changes in nutrient levels.
h. Growth-inducing consequences.
i. Changes in water flow and temperature.
j. Loss of gravel recruitment to downstream areas.
k. Flow reductions and de-watering.
l. Secondary effects to salmonids such as disease (i.e., bacterial gill disease).
m. Delay in sandbar breaching.

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Assessing the Draft Conservation Lands Network for Riparian and Fish
Viability
The Upland Habitat Goals stream, native fish and riparian habitat conservation targets are consistent
with the NMFS viability factors of key habitat and population. Furthermore, the methodology used to
select a network of conservation lands is deliberately designed to avoid many of the viability threats
detailed above. The Conservation Suitability layer used in the site selection software (Marxan) offers a
rough measure of watershed and ecological integrity by combining population density, average
distance to paved roads and parcelization into a single index. The software is directed to select areas
of high suitability. Deviations from this directive occur in a few areas where high priority targets with
a goal of conserving 90% of the remaining vegetation type or conservation element forces the software
to select areas of lower suitability to meet the 90% goal. For example, Marxan selected mapped
riparian forests along stream corridors in the suburbanized Santa Rosa area and in the urbanized Santa
Clara Valley landscape unit because riparian habitat is a Rarity Rank 1 with a 90% conservation goal.
To further assess conservation target viability, a watershed integrity analysis was undertaken to
identify the most suitable regions for the conservation of fish and riparian resources, and highlight the
stewardship challenges specific groups of watersheds sharing similar integrity factors.
Watershed Integrity Cluster Analysis

It is worth noting again that the coho recovery plan views the primary threats to viability to be roads
and railroads, droughts (particularly from the Russian River south), residential and commercial
development, logging and wood harvesting (particularly from the Russian River north). Channel
modification, livestock farming and ranching are significant threats in some watersheds. To gain a
better understanding of where threats may be of more concern, a watershed integrity cluster analysis
was completed by mapping factors representing some of these threats at the CalWater 2.2.1 Planning
Watershed level (PWS). Multiple factors affect each watershed so a cluster analysis was employed to
group similarly impacted PWS to more effectively map threats to integrity and identify appropriate
management actions across the study area.
The analysis used hierarchical clustering in the statistics program JMP 8.0 based on the following
threats calculated for each PWS:
1. Residential and Commercial Development.

i. Percent urban land coverage from FMMP 2006.
ii. Population density, log transformed from USGS Dasymmetric map of 2000 population in the
nine Bay Area counties. The logarithmic transformation stretches out the distribution and
better distinguishes urban, suburban, and exurban development.
2. Agricultural Practices. Percent Cultivated Agriculture land coverage from the California
Department of Conservation Farmland Mapping and Monitoring Program (FMMP) 2006.
3. Roads and Railroads. Distance to Roads, from USGS.
4. Logging and Wood Harvesting. Percent land coverage in Timber Harvest Plan (THP) from
CALFIRE to identify areas of active commercial and non-commercial forestry.
5. Fire. Post-fire erosion potential from CALFIRE, an application of the Universal Soil Loss
Equation (USLE) which takes into account slope steepness, soil type, and rainfall potential.

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Map 11. Watershed Integrity Cluster Analysis

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The cluster analysis identified eight clusters of relevance to Upland Habitat Goals. Map 11 highlights
the location of the clusters. Table 9 contains the number, area and relative measures of threats for each
of the clusters. Relative measures (High, Medium and Low) were determined by expert opinion
(Stuart Weiss, Ph.D., Upland Habitat Goals Science Advisor) after examination of the cluster diagrams
and diagnostics.
Table 9. Watershed Integrity Cluster Analysis

Distance
# of Pop Post-Fire
Cluster Acres % Urban % Ag from % THP
PWS Density Erosion
roads
Near Wilderness 48 338,264 L L L L L H
Wildlands 48 311,368 L L L M L H
Forestry 31 170,334 L L M M H H
Rural 211 1,267,389 L L M M L M
Suburban 62 552,628 M L H M L L
Urban Plains 42 686,233 H L H H L L
Hillside Agriculture 51 467,452 L H M M L M
Valley Agriculture 22 728,369 M H H H L L
Relative Threat Level: L = low, M = medium, H = high
Each cluster type has a distinct characteristics and complement of threats:
1. Near Wilderness: Forty eight PWS and 338,264 acres fell into this category characterized by
steep terrain with few roads and very low population density. These are the most intact PWS
where the primary land use is ranching and large tracts have already been conserved. These areas
appear to comprise headwaters and are found mostly in the Berryessa, Coyote Creek, and
Alameda Creek Hydrologic Areas (Mt. Hamilton and Blue Ridge Berryessa landscape units) in the
northeastern and eastern/southeastern regions of the study area. The steep slopes and remoteness
keep the threat of residential and commercial development low. Post-fire erosion potential also
appears high with the potential for livestock grazing and roads to also contribute to erosion.
Because Near Wilderness areas coincide with headwater areas, conservation actions should focus
on maintaining the high ecological integrity through fee or conservation easement acquisition and
land use policies. Stewardship should focus on best management practices for livestock grazing,
restoration of degraded riparian zones where necessary and erosion control from roads.
Under the current Draft Conservation Lands Network, a total of 274,877 acres are proposed for
protection in the Near Wilderness cluster type which includes 158,868 acres of already conserved
land.
2. Wildland: These forty eight PWS encompassing 311,368 acres are also in steep terrain, but with
more roads than Near Wilderness, are distributed more widely throughout the study area but
primarily near the outer boundaries. As is the case in the Near Wilderness Areas, these are highly
intact PWS with livestock grazing as the predominant land use and little threat of commercial and
residential development due to the steep and remote terrain. Roads and post-fire erosion emerge
as the primary threats.
Recommended conservation actions in Wildland Areas are the same as for Near Wilderness areas:
Focus on maintaining the high ecological integrity through fee or conservation easement

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acquisition and land use policies. Stewardship should focus on best management practices for
livestock grazing, restoration of degraded riparian zones where necessary and erosion control from
roads.
protection in the Wildland cluster type which includes 103,953 acres of already conserved land.
3. Forestry: Thirty one PWS and 170,334 acres make up this smallest category represented by
active or recently active Timber Harvest Plans posing a possible threat from logging, steep terrain
and medium population density but no urban or cultivated agricultural areas. These rugged PWS
are located primarily in the Gualala River HA (Sonoma Coast Range landscape unit) with a
smaller area in San Mateo Coastal, San Gregorio Creek and Pescadero Creek HAs (Santa Cruz
Mountains North landscape unit). These high precipitation and rugged PWS support extensive
second growth redwood and Douglas-fir forests and are key coastal watersheds for steelhead and
coho. The highest threats come from logging and erosion, post-fire and otherwise, with medium
threats posed by more roads and a slightly higher population density. The historical legacy of
poor forestry practices has created long-term erosion issues, so that watershed-scale rehabilitation
and restoration is necessary. Many are in the Gualala River watershed, where a sediment TMDL
was established in 2001.
Recommended conservation actions include the purchase of working forest conservation

easements that embody sustainable forestry practices and have enforceable stream protections,
pushing CALFIRE to enforce stream protections in timber harvest plans, and encouraging the
adoption of best timber management practices. Restoration forestry, erosion control fixes for
roads and riparian zone restoration are all essential to restore these watersheds. High forest
productivity and carbon storage may provide opportunities for carbon offsets under the California
Air Resources Board Forestry protocols that could conceivably finance management
improvements and habitat restoration.
protection in the Forestry cluster type which includes 24,348 acres of already conserved land.
4. Rural: These 211 PWS, by far the largest cluster at 1,267,389 acres, are distributed across nearly
all landscape units and characterized by moderate population densities in hilly, but not
mountainous terrain. Rural residential development occurs along the major roads, but there are
virtually no urban or cultivated agricultural areas, and ranching is the major land use. Rural
sprawl, post-fire erosion as well as that caused by livestock grazing and roads are medium threats,
Working landscape conservation easements and the use of cooperative agreements that provide
incentives for private landowners to improve resource management practices will be especially
useful in maintaining viable grazing and improving management in Rural areas. Road erosion
control, riparian restoration, managing water diversions and withdrawals and the adoption of best
management practices for rangeland are important for maintaining and restoring ecological
functions. The Natural Resources Conservation Service and Resource Conservation Districts play
pivotal roles in these watersheds by working directly with landowners providing information and
financial assistance to improve natural resource management.
protection in the Rural cluster type which includes 462,199 acres of already conserved land.
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5. Suburban: Sixty two PWS comprising 552,628 acres are characterized by higher population
densities, some urban areas, more roads, little cultivated agriculture, low slopes and are distributed
on the urban fringes. Extensive suburban development with high population density, many roads,
and small urban centers present many threats for conservation targets. Flood control projects
have altered stream channels and riparian zones are often narrow. And yet many streams in these
areas are used by anadromous fish to reach upper watersheds, and support pockets of native fish
assemblages.
The purchase of fee or conservation easements is rarely feasible in Suburban areas so regulatory
and policy protections combined with public education efforts are the primary protection tools.
Slope ordinances can be especially effective in conserving headwater areas. Restoration in these
areas is critical to re-connect these areas to the upper watersheds. Conservation and restoration
opportunities will depend on close cooperation between property owners, Resource Conservation
Districts, local and regional watershed councils (i.e. Urban Creeks Council, Alhambra Creek
Watershed Planning Group), regional water quality control boards, water and flood control
agencies.
protection in the Suburban cluster type which includes 149,380 acres of already conserved land.
6. Urban Plains: These 42 PWS and 686,233 acres are the densely populated urban areas in
flatlands and do not include all the Urban areas designated in Map 10. These PWS have the most
highly modified stream systems with extensive flood control and channelization where riparian
zones are narrow or even non-existent. Many if not all stressors resulting from commercial and
residential development are present and yet some larger streams have regionally unique warm-
water fish assemblages. Fish passage to upper watersheds is high priority, as is restoration of
remnant riparian habitat. Urban runoff creates water quality problems. Numerous TMDLs are in
varying stages of completion or proposal including one completed TMDL for the
Diazinon/Pesticide Toxicity that addressed more than 30 impaired urban creeks or creek segments.
Numerous urban streams are proposed for listing due to impairment from trash.
As with Suburban areas, protection and restoration strategies will rely on strong, enforceable
policies at both the state and local levels, such as the listing of impaired streams under the Clean
Water Act, and aggressive public education programs epitomized by the storm drain stenciling
programs administered by numerous regional and local entities. Success will require close
cooperation between landowners, city and county clean water programs, regional water quality
control boards, water and flood control agencies, and local and regional watershed councils (i.e.
Urban Creeks Council, Friends of Five Creeks).
The Draft Conservation Lands Network does not include any acreage to be conserved in the Urban
Plains.
7. Hillside Agriculture: Fifty one PWS covering 467,452 acres occur mostly in the North Bay,
have medium population density, substantial cultivated agriculture (primarily, but not exclusively,
vineyards) and are located in moderately hilly terrain. Residential development and cultivated
agriculture have degraded many stream channels, especially first and second order streams below
the scale of NHD, removed riparian vegetation and altered stream channels, contributing to
sedimentation and elevated nutrient levels, and diverted water. Most of the important larger
watersheds have sediment TMDLs in place or pending. Sediment TMDLs are awaiting approval
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for both the Napa River and Sonoma Creek and nutrient TMDLs are in development for these
same watersheds. Fish passage to upper watersheds is high priority.
Comprehensive, broad-based watershed plans can address some of the problems noted above such
as implementation of approved TMDLs. Slope ordinances, effective best management practices
for agriculture and erosion plans for vineyards and other cultivated agriculture are especially
important in these watersheds, as are irrigation and crop protection water withdrawals at key times
of the year. The Natural Resources Conservation Service, Resource Conservation Districts, and
collaborative programs such as the Fish Friendly Farming certification program can implement
watershed scale restoration. Rural residential impacts can be managed with local and regional
policy protections such as zoning restrictions and riparian protection ordinances.
protection in the Hillside Agriculture cluster type which includes 83,169 acres of already
conserved land.
8. Valley Agriculture: The twenty two PWS comprising 728,369 acres are intensively modified
flatlands with a cultivated agricultural matrix with urban and suburban patches of high population
densities. They are found in most valleys that are not intensively urbanized in the North Bay,
Central Valley fringe, and Santa Clara Valley, i.e., Santa Rosa and Brentwood. Streams and
wetlands have been extensively modified by flood control actions, channelization, water
withdrawal, gravel mining and other actions associated with agricultural practices and commercial
and residential development. Fish passage to upper watersheds is especially important, because
there are many potential impediments and diversions in these heavily developed lower watersheds
and wetlands near the Bay provide important rearing habitat for steelhead and salmon.
Agricultural and urban water quality impacts are high. Valley Agriculture/Urban areas in Napa
and Sonoma Counties comprise the best remaining baylands-uplands transitions that are expected
to shift upwards as the lowest elevations are inundated with sea level rise. Many of the PWS are
owned by public resource agencies such as the U.S. Fish and Wildlife Service or conservation
nonprofits including the Sonoma Land Trust.
The purchase of agricultural conservation easements that prescribe riparian and wetlands
protections are one protection option in these areas. Regulatory and voluntary programs and
policies are also an important tool in these areas. As with Hillside Agriculture areas, the Natural
Resources Conservation Service, Resource Conservation Districts, and collaborative programs
such as the Fish Friendly Farming certification program can build political will to restore riparian
and wetland areas.
protection in the Valley Agriculture cluster type which includes 67,358 acres of already conserved
land.
Watershed Integrity Cluster Gap Analysis

In order to evaluate the relationship between the Draft Conservation Lands Network and the watershed
integrity clusters, a gap analysis was completed. The distribution of land uses and levels of protection
for each watershed integrity cluster type are shown in Figure 3, using the same color scheme as in the
Planning Watershed gap analysis. The analysis shows that 81% of the Near Wilderness and 79% of
Wildland watershed areas, the most intact watersheds, are protected by the Conservation Lands
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Network, with remainders of ~60,000 acres in each cluster type. Rural watersheds have the greatest
area, and the Conservation Lands Network protects 67% of the area with a large remainder of 361,000
acres. Forestry watershed area is protected at 73%, with a remainder of 37,000 acres. 48% of
Suburban watershed area is protected these areas obviously are the open spaces outside of the
developed portions, with a remainder of 139,000 acres. Urban and Valley Agriculture are protected by
the Conservation Lands Network at 10% and 19%, respectively the areas available for conservation
are limited, and even those areas have lower suitability for conservation because of the population
density, roads, and parcelization.
Figure 3. Watershed Integrity Cluster Analysis
Land Use X Watershed Integrity Cluster

1,400,000
1,200,000
1,000,000
800,000 Remainder
600,000 Cultivated
RR10
400,000
Urban
200,000
CLN Additions
0 Protected BPAD

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VIII. Recommended Conservation Actions

The San Francisco Bay Area has a history of broad-based conservation collaborations successfully
tackling ambitious goals, such as the San Francisco Estuary Project and the South Bay Salt Ponds
Restoration. Achieving the Upland Habitat Goals fish and riparian goals requires a similar
commitment to collaboration by public agencies, private conservation organizations and landowners
with divergent missions. It is not feasible or realistic to acquire fee interests or conservation easements
for the entire stream network making the use of incentives and strong policies backed by enforcement
invaluable conservation tools. Cooperation is also essential to accomplish the extensive ecological
restoration that must occur if riparian habitats and ecological processes and functions are to be
restored.
The Riparian/Fish Focus Team developed nine recommended conservation actions to guide
conservation practitioners toward the goals outlined above.
Recommended Conservation Actions
1. Implement the Recovery Plan for Evolutionarily Significant Unit of Central California Coast Coho
Salmon and the Priority Recovery Actions for the Central California Coast Steelhead Distinct
Population Segment.
2. Focus initial efforts on Priority 1 Streams that are Core Areas in the Central California Coast Coho
ESU Recovery Plan and essential streams in Anchor Watersheds identified in Becker et al 2007.
3. Encourage the development of comprehensive, multi-stakeholder watershed plans that forge the
partnerships vital to coalescing action around large, complex issues.
4. Secure sensitive undeveloped headwaters and streamside lands through easements and fee
acquisition.
5. Limit further encroachment of riparian areas by establishing and enforcing strong policies that
mandate stream protections.
6. Restore stream channels and adjacent riparian habitat, including the strategic removal of barriers
to fish passage where appropriate.
7. Implement aggressive sediment and non-point source pollution control measures.
8. Secure seasonal water releases to benefit native fishes, especially for coho and rearing and
smolting steelhead.
9. Improve the stewardship of streams and riparian areas on public and private land.
Implementing these recommendations entails a range of actions from outright purchase to watershed
plans to enforcing stream protection regulations. Each action is discussed in more detail below.
1. Implement the Recovery Plan for Central California Coast Evolutionary Significant Unit of
Coho Salmon (March 2010) and the Priority Recovery Actions for the Central California
Coast Steelhead DPS.
The National Marine Fisheries Service released the Public Draft Recovery Plan for Central California
Coast Coho Salmon in March 2010. The plan is available for review and download at
http://www.dfg.ca.gov/fish/Resources/Coho/SAL_CohoRecoveryRpt.asp. The plan has extensively
detailed sections for each of the twenty eight priority watersheds with very specific recommended

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actions that will not be duplicated here. Ten of these twenty eight watersheds fall within the Upland
Habitat Goals study area and Upland Habitat Goals users are strongly encouraged to review the plan
for specific actions in their watersheds of interest. The recovery plan lists eleven highest priority
recovery actions important for success as follows:
Priority Recovery Actions for Central California Coast Coho Salmon ESU:
a. Finalize and implement the State Coastal Monitoring Plan. Implementation of the State Coastal
Monitoring Plan is essential for evaluating the long-term viability of CCC coho salmon and their
habitats as well as other species of listed salmonids in California.
b. Focus restoration funds, notably the Pacific Coast Salmon Restoration Fund and Californias
Fisheries Restoration Program, to prioritize funding in Core areas and on activities that will
increase the probability of freshwater survival.
c. Promote restoration projects in over-wintering habitats such as alcoves, backchannels, off channel
areas and estuaries.
d. Encourage appropriate agencies to secure funding for, and engage in, full enforcement of relevant
laws, codes, regulations and ordinances protective of coho salmon and their habitats.
e. Work with the Department of Fish and Game to improve freshwater sport fishing regulations to
minimize unintentional and unauthorized take, and incidental mortality, of CCC coho salmon by
anglers during the CCC coho salmon migration period.
f. Urge the California Board of Forestry to develop no-take rules and/or apply for a statewide
Forestry Habitat Conservation Plan and seek funding opportunities to support the effort.
g. Assess and address the mechanisms driving forest conversions and provide incentives for
sustainable forestry.
h. Encourage forestry landowners to develop HCPs protective of coho salmon and their habitat.
i. Improve coordination between the agencies, particularly the State Water Resources Control Board,
to effectively address seasons of diversion, off-stream reservoirs, and bypass flows fully protective
of CCC coho salmon.
j. Encourage counties to control forest conversion and prioritize development of rezoning and
grading ordinances that are protective of CCC coho salmon and their habitats.
k. Finalize the Mendocino Redwood Company Habitat Conservation Plan.
The recovery planning process has barely begun for the threatened Central California Coast Steelhead
DPS with only the Recovery Outline completed in 2007. The Department of Fish and Game
completed the Steelhead Restoration and Management Plan for California in 1996 and it is available at
http://www.dfg.ca.gov/fish/Administration/Grants/FRGP/Moreinfo.asp. In spite of the slow progress
on a recovery plan, several priority recovery actions have been stipulated for steelhead by NMFS
which overlap with those for coho (http://swr.nmfs.noaa.gov/recovery/Steelhead_CCCS.htm).
Priority Recovery Actions Needed for Steelhead:

a. Research and monitor distribution, status, and trends of steelhead.
b. Promote operations of current recovery hatcheries and develop Hatchery and Genetics
Management Plan (HGMPs) to minimize negative influences of hatcheries.

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c. Improve freshwater habitat quantity and quality.

d. Protect and restore habitat complexity and connectivity from the upper watershed to the ocean.
e. Conduct focused freshwater habitat restoration in anadromous salmonid streams (e.g., erosion
control, bank stabilization, riparian protection and restoration, and reintroduction of large woody
debris).
f. Balance water supply and allocation with fisheries needs through a water rights program,
designate fully appropriated watersheds, develop passive diversion devices or offstream storage,
eliminate illegal water diversions, and improve criteria for water drafting and dam operations.
g. Improve agricultural and forestry practices, in particular, riparian protections, road construction,
and road maintenance.
h. Improve county/city planning, regulations (e.g., riparian and grading ordinances) and county road
maintenance programs.
i. Remove/upgrade high-priority man-made fish passage barriers (e.g., watercourse crossings and
non-hydropower dams).
j. Screen all water diversion structures.

k. Replace existing outdated septic systems and improve wastewater management.
l. Identify and treat point and non-point source pollution of streams from wastewater, agricultural
practices, and urban environments.
m. Modify channel and flood control maintenance and eliminate artificial breaching of sandbars for
improvements in channel and estuarine habitats.
2. Focus initial efforts on Priority 1 Streams that are Core Areas in the Coho Recovery Plan
or Essential Streams in Anchor Watersheds per Becker et al. 2007.
Initial conservation actions should focus on Priority 1 Streams identified as Core Areas or Essential
Streams because of their significance to restoring sustainable populations of steelhead and coho whose
presence are an indicator of ecological health therefore benefiting other native fish. Becker et al. 2007
notes that restoration actions in non-anchor watersheds should not be ruled out, but the approach taken
in their study and in recovery planning is to focus on larger watersheds with independent populations
of steelhead with the highest probability of producing juvenile steelhead. The study further suggests a
similar analysis that uses assemblages of native fish instead of steelhead as the basis of a restoration
strategy.
However, opportunities to conserve habitat for other native fish populations should also be explored
because not all streams were evaluated for inclusion as essential streams because habitat
characterizations were not available. Map 3 shows Priority 1 streams and Appendix A lists Priority 1
and 2 streams.
3. Encourage the development of comprehensive, multi-stakeholder watershed plans.

Watershed planning processes, when well-executed, comprehensive and inclusive of a diverse array of
interests, can be the most effective approach to address the myriad of threats altering the biodiversity
values of stream corridors. The involvement of stakeholders from the agricultural, environmental,
urban, suburban and commercial realms often raises awareness of differing viewpoints, impacts on
riparian resources and can lead to collaborative solutions. In Becker et al. 2007, the authors note the
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significant increase in the probability of successful protection and restoration actions in watersheds
with comprehensive plans in part due to the enormous political will that is needed to undertake large-
scale restoration efforts. Watershed plans have been completed for many watersheds in the Bay Area.
A list of creek and watershed organizations and a description of their activities can be found at
www.alamedacountywatersheds.org. Nearly all of the Anchor and coho recovery plan watersheds
have a watershed plan or planning process underway involving many watershed councils and creek
groups. Because of the detail provided in most watershed plans, conservation practitioners are
encouraged to review watershed plans, where they exist, for more specific conservation action
recommendations.
Two regional planning documents were completed with diverse stakeholders offer directives to restore
the ecological health of streams and riparian ecosystems: the Comprehensive Conservation and
Management Plan and the Integrated Regional Water Management Plan.
Comprehensive Conservation and Management Plan (CCMP). In 1993, the San Francisco
Estuary Project, under the U.S. Environmental Protection Agency, completed the far-reaching
Comprehensive Conservation and Management Plan (CCMP) for the San Francisco Estuary. The plan,
mandated by the 1987 reauthorization of the Clean Water Act, incorporates actions for the nine Bay
Area counties and Yolo, Sacramento and San Joaquin counties and covers nine programs areas:
Aquatic Resources, Wildlife, Wetlands Management, Water Use, Pollution Prevention and Reduction,
Dredging and Waterway Modification, Land Use and Watershed Management, Public Involvement
and Education and Research and Monitoring. Many federal, state and local agencies and nonprofits
organizations were engaged over a 5-year period to craft the final recommendations, and forty two
signed the final plan. The San Francisco Bay Regional Water Quality Control Board was given the
lead for implementation with a pledge of continuing assistance from federal agencies.
The San Francisco Estuary Project (SFEP), now called the San Francisco Estuary Partnership, remains
active in the pursuit of CCMP implementation. Hosting periodic conferences to present issues,
progress and solutions, the SFEP also tracks progress toward CCMP implementation and updated the
plan in 2007. The 2007 updated CCMP added a new section on climate change and is available at the
SFEP website www.sfestuary.org.
The CCMP and the 2007 Update go into great detail describing issues and actions for each of the nine
program areas. Specific actions are called out in the recommendations below but conservation
practitioners are encouraged to review relevant sections when planning conservation actions.
San Francisco Bay Area Integrated Regional Water Management Plan. The Integrated
Regional Water Management Plan (IRWMP) was completed in 2006 and is a requirement for IRWMP
funding from Proposition 50, the 2002 Water Quality, Supply and Safe Drinking Water Projects,
Coastal Wetlands Purchase and Protection Bond Act and from Proposition 84; as well as other funding
from other state grant programs. The planning process brought together water, wastewater, flood
protection, and storm water management agencies, cities and counties, watershed management
interests and non-governmental environmental organizations to address a myriad of water issues and
identify water and habitat restoration and acquisition. The plan encompasses four functional areas of
regional water resources planning: Water Supply and Water Quality, Wastewater and Recycled Water,
Flood Protection and Storm Water Management, and the Watershed Management and Habitat
Protection and Restoration. Functional area reports describe the status, issues, impacts, recommended
actions and projects that should be funded by Prop 50 and offer a wealth of information. The entire
report is available at www.bairwmp.org.
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The IRWMP emphasizes the integration of multiple water management strategies on individual
projects, i.e., designing flood control measures to incorporate groundwater recharge, water quality
improvement measures, and restoration of riparian and wetlands habitat.. In addition, the IRWMP
promotes regional water management strategies, e.g., building interties between water supplies or
developing regional water conservation campaigns. A list of 127 initial projects that meet the IRWMP
criteria are included in the plan and recommended for funding. Opportunities to modify the
recommended list of projects will occur approximately every five years or as Prop 50 and Prop 84
IRWMP funds become available. The IRWMP also offers a detailed description of water management
strategies that provide benefits for fish and riparian resources.
4. Secure sensitive undeveloped headwaters and streamside lands through easements and
fee acquisition.
The protection of headwaters is particularly important because of the correlation between conserved
headwaters and healthy assemblages of native fish (Leidy, 2007). Numerous studies have found the
protection of headwaters is also vital to successful restoration efforts. Becker et al, 2007 cites a Pacific
Rivers Council report (Doppelt et al 1993, p. 33-34) describing the significance of these areas to
stream ecosystem viability. Disturbances in the headwaters can diminish or negate benefits conferred
by downstream restoration. Many headwaters are already in public or conservation ownership but
unprotected areas can be conserved using acquisition of fee or conservation easement interests by
public resource agencies or conservation nonprofits.
Funding for fee or easement acquisition is available from a variety of federal, state and local agencies
such as the US Fish and Wildlife Service, the California Wildlife Conservation Board and the
California Coastal Conservancy, California State Parks, regional park districts and private foundations.
Acquiring fee or conservation easement interests is not always possible for all stream segments
especially in the lower reaches where there is typically more development. If acquisition is not a
feasible or desirable option, cooperative agreements and cost-sharing programs for private landowners
offered by the Natural Resources Conservation Service, resource conservation districts or the US Fish
and Wildlife Service Partners for Wildlife Program can also be used to successfully protect and restore
riparian resources at least on an interim basis.
As noted previously, priority should be given first to the Anchor Watersheds and Essential Streams
from Becker et al. 2007), the CCC Coho Recovery Plan priority watersheds, and other watersheds that
may be identified as priorities as more stream habitat is characterized for available and suitable habitat
for steelhead, coho or other native fishes.
Many streams are encumbered by easements for flood control purposes. Little is known about these
easements and the rights associated with them such as the ability to remove vegetation or riprap banks.
While it would be a daunting task, it has been suggested that an inventory and evaluation be made of
these easements to determine their potential for providing any streamside protections for habitat
values.
5. Limit further encroachment of riparian areas by establishing and enforcing strong policies
that mandate stream protections.
Upland Habitat Goals recommends the use of existing regulations and the adoption of ordinances and
zoning designations where needed to protect, and in many cases, allow for the restoration of ecological
functions of riparian corridors. Stream protection policies and ordinances are the first line of defense,

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and often the only defense, for streams and riparian corridors traversing urban and suburban areas on
their way to the Bay. Fee and easement acquisitions are rarely a viable option in developed areas
where numerous small parcels abut a stream. Strong policies and regulations, including designation of
buffer areas, restrictions on removal of riparian vegetation, planting of non-native species, use of
pesticides, etc., backed by rigorous enforcement are critical in these developed regions.
The following actions are recommended to maximize the efficacy of policies and regulations in the
conservation of stream corridors.
a. Enforce existing regulations and policies. Numerous stream protection regulations are in place
at the federal, state and local levels for riparian habitat and water quality. A brief listing of these
regulations and policies follow.
i. Federal Regulations. At the federal level, the Army Corps of Engineers and the U.S. EPA
share responsibility for enforcing Sections 404 and 401 of the federal Clean Water Act.
Section 404 regulates the filling of wetlands and other waters while Section 401 requires
federal agencies to obtain certification from the state before issuing permits that would result in
increased pollutant loads to a waterbody including streams. Sections 401 and 404 are aimed at
water quality impacts but often require streamside protections because of the direct relationship
to water quality.
The US Fish and Wildlife Service can also provide some protections for riparian habitat
through the designation of critical habitat for threatened and endangered species such as the
California tiger salamander and Alameda whipsnake.
The National Oceanic and Atmospheric Administration National Marine Fisheries Service
(NMFS) uses the Magnuson-Stevens Fishery Conservation and Management Act, the Marine
Mammal Protection Act, and the Endangered Species Act to protect marine and riparian
ecosystems. NMFS is charged with drafting recovery plans for federally listed species and is
in the process of finalizing a recovery plan for the Central California Coast coho salmon ESU.
ii. State Regulations. State regulations protecting riparian areas come from several agencies:
Coastal Commission, State Water Resources Control Board through the regional boards, the
Bay Conservation and Development Commission and Department of Fish and Game.
State Water Resources Control Board and Regional Boards. As the name implies the State
Water Resources Control Board and the Regional Water Quality Control Boards focus on
water quality protection. The Upland Habitat Goals study area is predominantly within the San
Francisco Bay Regional Water Quality Control Board jurisdiction but parts of northern
Sonoma and Napa Counties are in the North Coast Regional Board jurisdiction, while a small
portion of southern San Mateo and Santa Clara Counties fall within the Central Coast Regional
Water Quality Control Board boundary. Many regulations governing these agencies authority
deal with point and non-point source pollution controls which will be discussed later, but the
protection of stream corridors also falls within their jurisdiction because of vital contributions
to water quality. The North Coast and San Francisco Bay Regional Boards, in conjunction
with the State Water Resources Control Board are developing a Stream and Wetlands System
Protection Policy to further the goal of protecting and restoring the physical characteristics of
stream and wetlands systems - stream channels, wetlands, riparian areas, and floodplains -
including their connectivity and natural hydrologic regimes, to achieve water quality standards
and protect beneficial uses.
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Department of Fish and Game. The Department of Fish and Game has several programs that
regulate activities that impact fish and wildlife resources within the Environmental Review and
Permitting division. The California Endangered Species Act and California Environmental
Quality Act are used to regulate activities that affect state-listed threatened, endangered, or
candidate species. The Lake and Streambed Alteration Agreement for an activity that will
substantially modify a river, steam or lake. Through its Timberland Conservation Program, the
Department may issue permits for road construction across streams when endangered species
habitat will be impacted.
California Coastal Commission. The Commission, under the 1976 California Coastal Act, is
charged with addressing numerous coastal issues including terrestrial and marine habitat
protection, landform alteration, commercial fisheries and water quality. The Coastal
Commission works in partnership with coastal cities and counties using Local Coastal Plans to
plan and regulate the uses of coastal lands within the Coastal Zone, which extends the length of
the state and varies in width from a few blocks to several miles inland. Local Coastal Plans
include zoning ordinances that allow for enforcement of the protections. According to a study
completed by for Fishnet 4C (Harris et al 2001), salmonids receive the best protection within
the Coastal Zone and the study recommended extending these protections further inland.
Bay Conservation and Development Commission. Authorized by the McAteer-Petris Act of

1965, BCDC regulates shoreline uses around the San Francisco Bay as well as portions of most
creeks, rivers, sloughs and other tributaries that flow into San Francisco Bay. The agency is
also the federally-designated state coastal management agency empowered to use the authority
of the federal Coastal Zone Management Act for this segment to ensure that federal projects
and activities are consistent with the policies of the Bay Plan and state law.
CAL FIRE and State Board of Forestry and Fire Protection. CAL FIRE oversees
Californias forest practice regulations which guide timber harvesting practices on private
lands. The government-appointed State Board of Forestry and Fire Protection within CAL
FIRE sets forest protection policies for the state. The California Forest Protection rules
provide many protections for streams and riparian habitat. Unfortunately, stream protections
are not always enforced.
iii. Land use policies and ordinances. The adoption of land use policies and implementing
ordinances protective of riparian corridors by cities and counties are important tools.
Numerous cities and counties have included stream protection and buffer policies in their
general plans and some have enacted ordinances to implement these protections. A 2004
survey conducted by the San Francisco Bay Regional Water Quality Control Board (Regional
Board, 2004) found that roughly 31 of the 85 cities within its jurisdiction had some form of
stream buffer policy in their municipal code, zoning ordinance, general plan or other policy
document. Six out of eight counties have established stream buffer policies, but the study does
not address how and if these policies are enforced.
The City of Oakland has found that requiring a permit for any work near a creek has enhanced
its ability to protect creeks and riparian areas (Estes pers comm. 2010). The city amended its
Stormwater Ordinance in 1997 to include creek protections and require a permit. While some
landowners contest the permit, Lesley Estes with the Citys Environmental Services Division
notes that a majority comply with the requirements.

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Slope or hillside development ordinances can be especially effective at reducing impacts to

riparian zones (Estes pers comm. 2010). Reducing the density and types of development when
slopes exceed a specified percent limits loss of habitat as well as the amount of runoff and
sedimentation. The City of Pleasanton uses a complex formula to calculate a weighted
incremental slope to determine how much of a parcel can be developed. In short, steeper
slopes are generally given lower densities.
The FishNet 4C project undertook an assessment of the general plans and implementing
ordinances of its six member counties - Mendocino, Sonoma, Marin, San Mateo, Santa
Cruz and Monterey. Fishnet 4C was initiated by the county supervisors in 1998 in response to
the federal listing of the coho and steelhead. The detailed and comprehensive assessment was
completed by UC Berkeley and FishNet 4C in 2001 (Harris et.al. 2001). Using a collaborative
approach involving a long list of public and private partners, FishNet 4C identified fifteen
highest priority actions that underscore the policy and management gaps in habitat protection
identified by the assessment. . The counties and their many partners are working implement
these actions.
FishNet 4C Priority Actions
1. Critical Fish Streams. Identify and map anadromous fish streams and tributaries in all
counties and make information available to county staff. Develop a strategy in each
county for prioritizing fish protection and restoration actions within watersheds and
throughout the county.
2. Coastal Zone Protections. Extend Coastal Zone resource protection policies to non-coastal
areas, where applicable and feasible, including wetland and riparian protection, sensitive
habitat protection, and grading and erosion control.
3. Riparian Buffers. Establish riparian protection areas to protect stream function that
prohibit new development and enforce these protections with ordinances. Where feasible,
buffer areas should be defined by the geomorphic floodplain. Seek funds to purchase
properties or easements where riparian protections make parcels unbuildable.
4. Bank Stabilization. Promote alternatives to conventional bank stabilization for public and
private projects and require evaluation of alternatives through the county permit process.
Consider a post-implementation audit review procedure to review completed projects.
5. Grading and Erosion Control. Develop grading and erosion control standards supported
by ordinances to minimize sediment impacts to anadromous streams, and provide adequate
staff to enforce the ordinances.
6. Wintertime Grading. Minimize winter grading and improve enforcement to eliminate

wintertime grading. Emphasize erosion control measures over sediment control.
7. Watershed Groups. Counties should support and be active members of multi-stakeholder

groups working on watershed issues, and commit county staff to participate.
8. Instream Flows. Support efforts and develop county programs to protect and increase
instream flows for anadromous fish. County efforts could include base flow monitoring,
protesting water rights, and working with water districts on conservation issues. Counties
should have policies to minimize impervious surfaces and promote surface water retention

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and condition developments that would divert or store surface water on the applicants
receipt of appropriative rights from the State Water Resources Control Board.
9. Roads. County public works, parks and open space district should inventory, evaluate and
fix problem roads which systematically contribute sediment into critical coho streams.
Counties should develop a program or policies for identifying especially unsuitable
existing development, infrastructure and road segments affecting anadromous fish streams.
Consider options and opportunities for restoring or gradually eliminating them.
10. Lagoon Breaching. Evaluate lagoon breaching policies where conducted within each
county and, if warranted, adopt policies and implement procedures that mitigate impacts to
anadromous fish.
11. Road Maintenance Standards. Develop and adopt written standards for county road
management practices, under both routine and emergency conditions. These standards
should include guidelines for road maintenance and construction that minimize
sedimentation and runoff impacts, and address storage and disposal of spoils, stream
crossings, culvert diversion potential, fish passage, and landslide and slope repair. County
staff should participate in trainings for the implementation of roads, culverts and
maintenance practice standards, developed to minimize impacts to the fishery.
12. Emergency Projects. Review how storm-damage related road, culvert and bank
stabilization projects were installed under emergency conditions, compared to non-
emergency installations.
13. Spoils Storage. Establish adequate spoils storage sites throughout the counties so that
material from landslides and road maintenance can be stored safely away from
anadromous streams. Coordinate these efforts with CalTrans.
14. Channel and Riparian Corridor Clearing. Reduce native riparian vegetation clearing and
sediment removal adjacent to and in anadromous fish streams. Retain large woody debris
within streams to the extent possible. When woody material is removed, it should be
stored and made available for stream enhancement projects.
15. Fish Migration Barriers. Develop a program to identify, evaluate and prioritize county
facilities that are barriers to salmonid migration. Develop a systematic program to seek
funding for replacement of these identified fish passage barriers. Commit to sending
county staff to trainings on fish passage guidelines and culvert design according to new
NMFS and CDFG standards.
The FishNet 4C counties are partnering with numerous public agencies and private
organizations such as CalTrans, resource conservation districts and Trout Unlimited to name a
few, to accomplish the priority actions.
Participants in the FishNet 4C Program include County Supervisors and staff from planning,
public works, parks, open space and water agencies. Several other agencies such as CalTrans,
National Marine Fisheries Service and the Department of Fish and Game, as well as many
nonprofit conservation organizations participate in achieving the FishNet goals. The counties
focus their efforts on services they provide that can affect salmonid habitat. These efforts
include:

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Implementing on-the-ground fish passage and restoration projects.

Employing best management practices during maintenance activities
Incorporating aquatic habitat protections into land use regulations and policies.
The FishNet 4C assessment did not include activities overseen by agencies other than the
county such as timber harvesting and agricultural practices. However, the CCMP recommends
counties enact timber harvesting and agricultural practices regulations to reduce impacts to
riparian processes and functions.
Stream Buffers
The Upland Habitat Goals recommends securing buffers as wide as possible whenever possible
because of the many ecosystem functions provided by riparian areas. However, in many
areas, increasing riparian buffers is constrained by development. The 2004 Regional Board
study found that in Bay Area cities with stream buffer policies, the buffer distances vary
greatly and approximately 38% required a 33-foot or greater minimum buffer difference. The
authors speculated that the distances were the result of political pressure rather than scientific
criteria underscoring the resistance that can be encountered when enacting stream protections.
Several studies articulate recommendations for riparian buffer widths based on the riparian
function under consideration. On such report, Comparison of Methods to Map California
Riparian Areas (Collins et.al.,.2006), by the San Francisco Estuary Institute (SFEI), conducted
an extensive literature review and developed the table in Table 10 describing riparian functions
and corresponding riparian widths highlighting the complexity of making stream buffer
recommendations.
Table 10. Riparian Buffer Width Recommendations

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Another study, Setback Recommendations to Conserve Riparian Areas and Streams in Western
Placer County (Jones & Stokes, 2005), offers an extensive analysis of ecological functions,
species requirements and human impacts. Two recommendations were made by the study:
1. For first and second order stream segments, a minimum riparian setback that includes the
entire active floodplain plus a buffer of 30 meters or 98 feet. The report notes that even at
this size, the buffer is not sufficient for wildlife with large area requirements.
2. For third order or greater streams and lower order stream segments adjacent to protected
lands, a setback of at least 100 meters or 328 feet from the active floodplain is
recommended for the purpose of conserving and enhancing stream and riparian ecosystem
functions including most wildlife habitat functions. If possible, 150 meters or 656 feet
would be even better.
A third study completed by Jones & Stokes for the Napa County Conservation Development
and Planning Department recommended different buffer widths depending on stream class on
the ecosystem functions to be protected.
Class I Streams. Class I streams are fish-bearing so buffers should be large enough to
encourage natural stream meander, contribute woody debris, develop mature riparian forest
(where applicable), moderate steam temperatures and facilitate wildlife migration and habitat
use. Buffers should range from 100 to 150 feet on the low end and 300+ feet on the high end.
Class II Streams. Class II streams are found higher in the watershed, do not have fish but host
a suite of other aquatic vertebrate species and have narrower riparian corridors due to limited
floodplain development. A minimum buffer width of 75 feet is recommended with additional
setbacks depending on the slope.
Class III Streams. These streams do not contain aquatic vertebrate or macro-invertebrate
species, are generally intermittent or ephemeral, and are the firsts point of entry of sediments
and/contaminants into the stream ecosystem. Stream buffers for Class III streams should
emphasize sediment and nutrient filtration and a bare minimum buffer of 25 feet is
recommended.
b. Coordinated public education program. Compliance with stream protection policies can be
improved when paired with a public education program explaining the significance of these areas.
Public education is especially important where streams reach exurban and urban areas because
enforcing such regulations on so many parcels is difficult to impossible.
Public education can be accomplished by city and county governments through a variety of means
ranging from inserts in utility bills, public meetings to the more aggressive public media campaign
envisioned the 2007 CCMP Update. In more rural areas, Resource Conservation Districts and the
Natural Resources Conservation Service play a vital role in not just educating property owners but
also providing technical assistance for resource conservation. The Napa Resource Conservation
District compiled a comprehensive guide for property owners entitled Caring for Creeks in Napa
County: Management Tips for Streamside Property Owners. The Alameda Countywide Clean
Water Program compiled the Creek Care Guide: A Guide for Residents in the San Lorenzo Creek
Watershed.

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c. Consider a program similar to the FishNet 4C Program for counties with creeks that drain
to the Estuary. Or Conduct a review of existing regulations and policies, determine most
effective, encourage adoption and enforcement.
6. Restore stream channels and adjacent riparian habitat, including the strategic removal of
structures where appropriate.
Once headwaters and key riparian corridors have been secured, or strong, enforceable policies are in
place, restoration of the riparian ecosystem should be undertaken so that impediments to ecological
functions can be removed. Doppelt et al 1993 advocate focusing restoration on relatively healthy
habitat then expanding to adjacent areas. Becker et al 2007 articulates a restoration strategy for
steelhead encompassing three areas.
1. Water Supply. Analyses providing quantitative estimates of adequate water supply for rearing
habitat and processes that implement these instream flow provisions must be developed for the
Anchor Watersheds.
2. Limiting Factors Analyses. Limiting factors analyses should be completed for at least the key
tributaries in the Anchor Watersheds and used to prioritize restoration activities.
3. Re-Connection to the Bay. A comprehensive and well-funded program is needed to re-connect

high quality spawning and rearing habitat to the Bay. The lower reaches of all the Anchor
Watersheds have been severely altered and will require strong political will and significant
funding to re-establish historic connections.
Barriers to fish passage are a significant threat to steelhead and coho salmon viability and present a
complex challenge to restoration advocates. Barriers can be the result of dams, water diversions,
poorly constructed roads, or culverts to name a few of the causes. Table 11 lists different types of
barriers from the California Fish Passage Assessment Database (August 2008) for each of the
CalWater 2.2.1 Hydrologic Areas. The table indicates that there are at least 2,116 barriers with higher
numbers in cultivated agricultural areas such as Fairfield and Amos-Ogilby Hydrologic Areas in
eastern Contra Costa County. The Anchor Watersheds and Essential Streams in Becker et.al., 2007,
were selected because steelhead rearing habitat was currently available or there was a strong possibility
that critical barriers would be removed. The Coho Recovery Plan descriptions and recommended
actions for the priority watersheds provide detailed information on fish passage barrier types and
locations.

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Table 11. Fish Passage Barriers in CalWater Hydrologic Areas

(California Fish Passage Assessment Database, August 2008)
Natural Natural
CalWater Hydrologic Partial Total Screened Unscreened
Limit to Partial TOTALS
Areas (v. 2.2.1) Barrier Barrier Diversion Diversion
Anadromy Barrier
Alameda Creek 1 13 14
Amos-Ogilby 2 6 322 330
Ano Nuevo 5 4 5 12 1 27
Berkeley 5 2 7
Berryessa 1 1
Bodega Harbor 0
Bolinas 2 2 4
Concord 1 8 1 5 15
Coyote Creek 2 39 7 48
East Bay Cities 1 11 59 21 92
East Rocky Ridge 1 1
Elmira 1 1
Estero Americano 0
Estero San Antonio 0
Fairfield 1 6 16 383 406
Fremont Bayside 0
Guadalupe River 2 51 11 64
Gualala River 8 3 1 12
Lower Putah Creek 1 1 15 17
Lower Russian River 3 4 48 11 4 17 87
Middle Russian River 8 4 70 28 3 21 134
Napa River 14 14 63 24 75 190
Novato 4 8 12
Pacheco-Santa Ana Creek 2 3 2 1 8
Palo Alto 2 2 72 22 98
Pescadero Creek 14 2 23 16 55
Petaluma River 3 3 13 10 3 32
Pinole 1 2 6 7 16
Point Reyes 1 1
Russian Gulch 2 2
Salmon Creek 7 2 3 1 13
San Francisco Bayside 0
San Francisco Coastal 0
San Gregorio Creeek 5 2 13 11 31
San Mateo Bayside 8 14 22
San Mateo Coastal 1 1 26 13 41
San Pablo Bay 3 3

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Table 11. Fish Passage Barriers in CalWater Hydrologic Areas (continued)
Natural Natural
CalWater Hydrologic Areas Partial Total Screened Unscreened
Limit to Partial TOTALS
(v. 2.2.1) Barrier Barrier Diversion Diversion
Anadromy Barrier
San Rafael 3 23 19 45
Santa Cruz 1 1
Santa Cruz Mountains 8 12 15 8 1 44
Sonoma Creek 35 69 25 10 139
South Santa Clara Valley 3 3
Suisun Bay 4 4
Suisun Bay - in Delta 5 5
Tomales Bay 2 4 53 28 87
Upper Putah Creek 0
Upper Ulatis 0
Watsonville 1 1 2 4
TOTALS 131 71 685 334 30 865 2,116
7. Implement aggressive sediment and non-point source pollution control measures.
Sedimentation and non-point source pollution result from numerous activities and are difficult to
control. The impacts are also widespread as indicated by the list of 270 impaired waterways in 88
water bodies (includes bays and estuaries) developed by the San Francisco Bay Regional Water
Quality Control Board under Section 303(d) of the Clean Water Act. Sedimentation and non-point
source pollutions problems in coastal watersheds also become apparent when reviewing specific
actions recommended under the Coho Recovery Plan. The plan recommendations mention a variety of
existing regulations and voluntary programs at all levels of government that can be tapped to address
the problem. As with many regulatory programs, enforcement capability is the key to success.
Many of the FishNet 4C recommendations and other regulations and policies aimed at protecting
streams and riparian resources noted previously include the reduction of sediment and non-point
source pollution. Coordination among agencies and enforcement of these measures could be improved
in many areas.
a. Enforce existing regulations and policies. Numerous water quality control regulations have
been enacted at the federal, state and local levels that aim to stem sedimentation and non-point
source pollution. To further complicate regulations, the nine counties of the Upland Habitat Goals
study area fall under the jurisdiction of three Regional Boards North Coast, San Francisco Bay and
Central Coast.
i. Federal Regulations. As noted previously, the Army Corps of Engineers and the U.S. EPA
share responsibility for enforcing Sections 404 and 401 of the federal Clean Water Act of
1972. Section 404 regulates the filling of wetlands and other waters while Section 401 requires
federal agencies to obtain certification from the state before issuing permits that would result in
increased pollutant loads to a waterbody including streams.

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Many cities and counties have formed countywide clean water programs to meet the
requirements of the Clean Water Act. The Contra Costa Clean Water Program includes the
County, nineteen cities and the Contra Costa Flood Control and Water Conservation District
have formed the Contra Costa Clean Water Program to eliminate stormwater pollution through
public education, inspection and enforcement activities, and outreach to local industries.
ii. State Regulations. The State Water Resources Control Board and its regional boards are the
primary enforcers of state water quality regulations under several different mandates.
Basin Plan. Each regional water quality control board is required to draft a Regional Water
Control Plan or Basin Plan that sets the States program of actions to preserve, enhance and
restore water quality in a specific region. The basin plan is the primary policy document
describing the legal, technical and programmatic bases for water quality regulation and
describes the beneficial uses for each water body, water quality objectives to protect beneficial
uses and implementation plans for achieving water quality objectives.
Section 303(d) Impaired Water Bodies List. The Clean Water Act of 1972 requires the State
Water Quality Control Board to evaluate the water quality conditions of rivers, streams, creeks,
bays and coastal areas in each region every two years. The Board must report its findings
(Section 305(b) water quality assessment) and provide a list of impaired water bodies (the
Section 303(d) list) to the U.S. EPA for consistency review and approval. The Regional Water
Quality Control Boards gather the information for the Section 305(b) assessments and 303(d)
list of impaired water bodies. An impaired water body is one that does not meet or is not
expected to meet water quality standards even after implementation of technology based
requirements of the Clean Water Act. The State Board submitted proposed changes and
additions to the 303(d) list for 2008 and U.S. EPA has not yet approved a final statewide list.
Once a proposed impaired water body is approved by the U.S. EPA, the regional board is then
required to develop a TMDL to address the impairment. TMDLs are action plans to restore
clean water that examine the water quality problems, identify sources of pollutants, and specify
actions that create solutions. TMDLs define how much of a pollutant a water body can tolerate
and meet water quality standards. TMDLs must account for all the sources of a pollutant such
as wastewater treatment facility discharges, runoff from homes, agriculture, and streets or
highways, "toxic hot spots, and airborne deposits. Once completed and approved, TMDLs are
adopted by the Regional Board as amendments to the regions Basin Plan. Regional boards
then must insure the implementation and ongoing monitoring of the adopted TMDLs.
Implementation can take several forms including Regional Board regulatory actions in the
form of permits, waivers or enforcement orders; regulatory actions by another federal, state or
local agency; or through non-regulatory actions.
The San Francisco Bay Regional Board approved a 303(d) list of impaired water bodies with
more than 270 listings in 88 water bodies in February 2009 and awaits US EPA approval of the
list. Regional Board staff are developing thirty TMDL projects to address more than 160 of
these listings leaving over 100 TMDLs yet to be started. Note that one TMDL for the
Diazinon/Pesticide Toxicity TMDL for urban creeks addressed more than 30 impaired creeks
or creek segments and that many new streams are being proposed for listing due to impairment
from trash. TMDLs, in various stages of implementation and completion, are listed below.

Page 67 of 76
At this time, the list of required TMDLs is outstripping the regional boards capacity to
complete them leaving a large backlog. The regional boards must revise the 303(d) lists every
two years and as a public process, conservation practitioners have the opportunity to suggest
streams and provide documentation of impairment.
Section 401 Certification. Regional Boards also manage the permitting process for discharges
to streams and wetland areas under the Section 401 of the Clean Water Act and the states
Porter-Cologne authority.
Section 319(h) Non-Point Source Pollution Grants. Section 319(h) grants are federally funded
and address non-point sources of pollution such as most farming and forestry operations.
Preference is given to proposals that implement TMDL recommendations.
iii.Land use policies and ordinances. Most of the recommendations described under limiting
further encroachment of creeks also prevent non-point source pollution and sedimentation.
The 2007 CCMP Update also provides a wealth of recommendations for actions that local
governments can take to reduce sedimentation and non-point source pollution including the
incorporation of stormwater management plans into general plans. It has been noted that
counties and cities with slope ordinances are much more successful in preventing impacts to
riparian areas (Pers.com. Lesley Estes, City of Oakland, July 6, 2010).
Many cities and counties come together to facilitate compliance with land use policies and
ordinances by providing training and education. The City of Oakland and the Alameda County
Flood Control and Water Conservation District have partnered to create the Collaborative Creek
Improvement Program to restore, preserve, and improve Oakland's creeks. The program
includes: implementation and training for alternative flood control, soil bioengineering training,
riparian restoration, illegal dumping mitigation, water quality improvement, and community
outreach and involvement. The projects are selected with community input and implement the
Citys Open Space, Conservation and Recreation general plan element and the Creek Protection
Ordinance.
b. Maximize use of existing voluntary incentive programs and increase financial support for
such programs. Programs that offer technical assistance and incentives to modify management
practices to reduce sedimentation and non-point source pollution can be effective. The Fish
Friendly Farming Certification Program (www.fishfriendlyfarming.org), run by the California
Land Stewardship Institute, exemplifies what can be accomplished with voluntary agreement.
Three resource agenciesthe Regional Water Quality Control Board, the National Marine
Fisheries Service, and the County Agricultural Commissionerprovide an objective third-party
certification to farmers in the North and East Bay regions. Fish Friendly Farming provides for
voluntary, self-directed compliance with the rigorous standards of state and federal water quality
laws (Clean Water Act), the federal Endangered Species Act, the state pesticide laws as well as
local regulations.
Programs offered by the Natural Resources Conservation Service, Resource Conservation Districts
and US Fish and Wildlife Service are covered in the improving stewardship discussion. These
programs offer assistance with management and restoration that contribute to reduced
sedimentation and non-point source pollution.

Page 68 of 76
Table 12. TMDL Projects in the Upland Habitat Goals Study Area
North Coast Regional Water Central Coast Regional
San Francisco Bay Regional
TMDL Status Quality Control Board Water Quality Control
Water Quality Control Board
(within study area) Board (within study area)
Completed Napa River Pathogens Gualala River Sediment
TMDL Projects San Francisco Bay Mercury Laguna de Santa Rosa
Sonoma Creek Pathogens Sediment and Nitrogen
Tomales Bay Pathogens Redwood Creek Sediment
Urban Creeks Diazinon/ Pesticide Stemple Creek & Estero de San
Toxicity Antonio Sediment, Nutrients
Walker Creek Mercury
TMDL Projects Guadalupe River Watershed
Awaiting Mercury
Approval from Napa River Sediment
Water Boards Richardson Bay Pathogens
and/or US EPA San Francisco Bay PCBs
Sonoma Creek Sediment
TMDL Projects Lagunitas Creek Sediment Laguna de Santa Rosa Pajaro River Watershed
in Development Pacifica beaches, San Pedro Phosphorus, Dissolved Oxygen, Siltation TMDL
Creek Pathogens TemperatureMark West Creek
Napa River Nutrients Sediment, Temperature
North San Francisco Bay Santa Rosa Creek Indicator
Selenium Bacteria, Sediment,
San Francisquito Creek Sediment Temperature
Butano and Pescadero Creeks Russian River (two reaches)
Sediment Indicator Bacteria
Sonoma Creek Nutrients
Tomales Bay Mercury
Tomales Bay Siltation/Sediment
Walker Creek Sediment
TMDL Projects Gualala River Temperature

Not Yet Begun Laguna de Santa Rosa Mercury
Redwood Creek Temperature
Russian River (all) Sediment,
Temperature
TMDL Projects Pajaro River Fecal Coliform
Approved by TMDL (including Pajaro
US EPA River, San Benito River,
Llagas Creek and
Tequisquita Slough)
Pajaro River (Including San
Benito River, Llagas Creek
and Rider Creek) Sediment
TMDL
Pajaro River (Including
Llagas Creek) Nitrate
TMDL

Page 69 of 76
c. Coordinated public education campaign. Drains to Bay storm drain stenciling campaigns.
Difficult to measure effectiveness but still important. . billboards as exemplified by the City of
Oaklands got oil? campaign Polling done around storm drain stenciling indicated a 75%
awareness level of the problems associated with dumping in storm drains.
d. Review existing programs?
8. Secure seasonal water releases to benefit native fishes, especially coho salmon and
rearing and smolting steelhead.
Securing seasonal water releases is vitally important to anadromous fish as well as to most native fish.
The descriptions in the Notes column of the Leidy 2008 Report included in Appendix B frequently
note that a stream or stream segment goes dry in the summer. Recovery actions for both coho and
steelhead recommend working with the State Water Quality Control Board to alter diversion dates and
allow releases at critical times.
Becker et al. 2007 recommends completing analyses to provide quantitative estimates of adequate
water supply for rearing habitat and processes that implement these instream flow provisions for at
least the Anchor Watersheds if restoration is to be successful.
Seavy et al notes that riparian areas could be further impacted if response to climate change is building
taller levees, deeper wells, and higher dams. Must engage with policymakers on water management
issues to blunt potential impact.
9. Improve the stewardship of streams and riparian areas on public and private land.
The Upland Habitat Goals project aims to restore all Bay Area streams to ecological health. This goal
cannot be accomplished solely through fee and conservation easement purchase. Even if it were
desirable or feasible to purchase fee or easement interests on all streams, promoting and providing
incentives for good stewardship would still be crucial to success.
Ensuring sound stewardship practices is vital to biodiversity conservation. Unless public and private
lands are managed for biodiversity values, protection does not mean successful conservation. The
recovery actions for both coho and steelhead advocate for improved agricultural and forestry
management practices to protect water quality and preserve riparian vegetation.
Private landowners play an important role in restoring and maintaining stream health and this is
especially true of the ranchers and forestland owners in the Bay Area. Large tracts of habitat are found
on ranches and forestland in the outer reaches of the study area. Numerous public programs offer
technical assistance and matching funds to implement habitat enhancement, erosion control, fencing
and other stream protection projects and are a cost effective means to improve stream health.
The Natural Resources Conservation Service (NRCS) offers several voluntary programs that provide
technical assistance and/or cost sharing to farm. Several of the programs require the property owners
to sign a contract or cooperative agreement for 5 to 10 years to insure that the improvements are
maintained for a specified period after completion.
Environmental Quality Incentives Program (EQIP). EQIP assists farmers and ranchers who want to
address natural resource concerns with technical and financial assistance. EQIP provides cost-share
funding to promote agricultural production and environmental quality as compatible goals. Eligible
projects include rangeland management activities such as cross-fencing, spring development, pipelines,
Page 70 of 76
tanks, troughs, prescribed grazing, water conservation projects such as irrigation improvements, and
wildlife habitat improvement (pond restoration, habitat management). Contracts for maintaining these
improvements run from 1 to 10 years in length.
Wildlife Habitat Incentives Program (WHIP). Another voluntary program, WHIP assists landowners
to develop and improve wildlife habitat primarily on private land. Through WHIP, NRCS provides
both technical assistance and up to 75 percent cost-share assistance to landowners and others to
develop upland, wetland, riparian, and aquatic habitat areas on their property. Landowners may enroll
privately owned land, federal land when the primary benefit is on private or tribal land, state and local
government land on a limited basis, and Tribal land. The program provides cost-share payments to
landowners under agreements that are usually 5 to 10 years in duration, depending upon the types of
practices to be installed.
Conservation Stewardship Program (CSP). The CSP program encourages producers to address
resource concerns by providing funding to support existing land stewardship as well as additional
conservation activities. The program employs 5-year contracts to provide annual payments to support
good land management. CSP provides opportunities to both recognize excellent stewards and deliver
valuable new conservation.
Grassland Reserve Program (GRP). The GRP offers landowners the opportunity to protect, restore,
and enhance grasslands on their property. The program emphasizes support for grazing operations,
plant and animal biodiversity, and grassland and land containing shrubs and forbs under the greatest
threat of conversion. The program offers several enrollment options: 30-year and permanent
easements; 10-year, 15-year, 20-year, or 30-year rental agreements; and restoration agreements which
may be used in conjunction with any easement or rental agreement. NRCS, Farm Service Agency and
USDA Forest Service coordinate the implementation of GRP.
US Fish and Wildlife Service Partners for Wildlife. The Partners for Fish and Wildlife Program is a
voluntary program offering technical and financial assistance to landowners who want to improve fish
and wildlife habitat on their lands. The program emphasizes the restoration of historic ecological
communities for the benefit of native fish and wildlife in conjunction with the desires of private
landowners. Assistance ranges from informal advice on the design and location of potential restoration
projects, to designing a project and funding up to 50% of the implementation costs. A cooperative
agreement is developed between the Service and the landowner that requires the landowner to maintain
the restored or improved site for a minimum of 10 years. Projects that receive the highest priority for
funding are those that provide direct benefits to migratory birds, anadromous fish, and threatened and
endangered species.
Habitat restoration and enhancement projects may include, but are not limited to, restoring wetland
hydrology; installing fencing along riparian areas to exclude livestock; rehabilitating in-stream aquatic
habitats; removing nonnative plants; planting native grasslands; and planting native trees, shrubs, and
other plants to provide food and shelter for fish and wildlife in degraded habitats.
The California Department of Forestry and Fire Protection or CAL Fire offers programs and funding to
improve stewardship of forestlands.
California Forest Stewardship Program (FSP). The FSP, encourages good stewardship of forests and
oak woodlands, and operates on a community or watershed scale. The program offers both technical
and financial assistance.

Page 71 of 76
California Forest Improvement Program (CFIP). CFIP provides financial assistance, in years when it
is funded, and is aimed at improving the economic value and environmental quality of forestlands.
CFIP matches up to 75% of costs for private lands including erosion control, revegetation, road
rehabilitation, and installation of structures such as waterbars, rocked crossings, etc. to reduce soil
erosion and stream sedimentation. CFIP also funds fish and wildlife habitat improvement, including
creation of corridors and openings, planting oaks or riparian species, installing exclusion fencing along
watercourses and wetlands, and stream restoration projects.
help rebuild forest and wildlife resources to meet our future needs for a healthy environment and
productive forests. Forest landowners can be reimbursed up to 75% of their expenses for the following:
Forest Stewardship Program (FSP). The FSP program requires a 50% from private landowners and is
designed to assist communities to more actively manage their watershed resources, to keep their forests
and associated resources productive and healthy, and to increase the economic and environmental
benefits of these resources.
California Department of Fish and Game Private Lands Management Program (PLM). The PLM was
initiated to offer landowners economic incentives to manage their lands for the benefit of wildlife.
Landowners who enroll in this ranching for wildlife program consult with biologists to make
biologically sound habitat improvements that benefit wildlife, like providing water sources, planting
native plants for food, and making brush piles for cover. In return for these habitat improvements,
landowners can charge fees for wildlife viewing, hunting and fishing.
UC Extension. UC Extension specialists offer technical assistance and workshops for farmers,
ranchers and forestland owners to improve management for both ecological health and productivity.
In urban and suburban areas, organizations such as the Urban Creeks Council and numerous watershed
councils and groups not only spearhead restoration and enhancement projects, they also serve a public
information function. These groups work with cities, counties and the general public to raise
awareness, provide information for property owners and undertake creek restoration projects. The
Urban Creeks Councils Streamside Management Program for Landowners operating in Contra Costa
County, Marin County Flood Zone 9, and Arroyo De La Laguna in Alameda County, courtesy of Zone
7 Water Agency
Good stewardship of lands already in public ownership is also critical. Public land managers often
lack sufficient funding to manage public lands optimally for fish and wildlife resources.
Forestry Best Practices recommendations.
Grazing Management Best Practices recommendations.
Additional Resources
Resources for Watershed Planning:

1. San Francisco Bay Regional Water Quality Control Board
http://www.swrcb.ca.gov/rwqcb2/water_issues/programs/watershed.
2. U.S. EPA Handbook for Developing Watershed Plans to Restore and Protect Our Waters,
March 2008, EPA reference number EPA 841-B-08-002,
www.epa.gov/owow/nps/watershed_handook.
3. Alameda County Watershed Forum website, http://www.alamedacountywatersheds.org.
4. The California Watershed Network, www.watershednetwork.org.

Page 72 of 76
5. The Watershed Portal, California Department of Conservation,

www.conservation.ca.gov/dlrp/watershedportal/Pages/Index.aspx.
Resources for Public Education:
IX. Data Gaps.

During the process of establishing goals for riparian and fish resources, several important data gaps
were identified. The Upland Habitat Goals is compiling these data gaps and they will be prioritized
and incorporated into the final report.
1. Comprehensive map of riparian habitat in the San Francisco Bay Area.
2. Complete a native fish assemblage-based restoration strategy similar to that employed by Becker
et.al., 2007 but using the information from Leidy 2007 (Becker et.al., 2007)
3. Survey cities and counties for adopted stream protection ordinances to determine gaps and develop
model ordinances and zoning regulations.
4. Map existing easements held by public agencies for flood management, groundwater recharge and
other public purposes. Need to understand how protective they are.

Page 73 of 76
X. References
Becker, G.S., I.J. Reining, D.A. Asbury, A. Gunther, Ph.D. 2007. San Francisco Estuary Watersheds Evaluation:
Identifying Promising Locations for Steelhead Restoration in Tributaries of the San Francisco Estuary, Center for
Ecosystem Management and Restoration.
California Department of Fish and Game, 2004. Recovery strategy for California coho salmon. Report to the California
Fish and Game Commission.
California Department of Fish and Game. 1996. Steelhead Restoration and Management Plan for California.
Collins, J.N., M. Sutula, E.D. Stein, M. Odaya, E. Zhang, K. Larned. 2006. Comparison of Methods to Map California
Riparian Areas. Final Report Prepared for the California Riparian Habitat Joint Venture.
Koehler, J. 2007. Napa River Fish Community Update, Napa Resource Conservation District.
Doppelt, B., M. Scurlock, C. Frissell and J. Karr. 1993. Entering the Watershed: A New Approach to Save Americas
River Ecosystems. Island Press. Washington, D.C.
Harris, R., S, Kocher. January 2001. Effects of County Land Use Policies and Management Practices on Anadromous
Salmonids and Their Habitat: Sonoma, Marin, San Mateo, Santa Cruz and Monterey Counties, California. University of
California, Berkeley, Department of Environmental Science, Policy and Management.
Jones & Stokes. 2005. Setback Recommendations to Conserve Riparian Areas and Streams in Western Placer County.
(J&S 03-133). Sacramento, CA.
Leidy, R.A. 2007. Ecology, Assemblage Sructure, Distribution, and Status of Fishes in Streams Tributary to the San
Francisco Estuary, California. SFEI Contribution #530. San Francisco Estuary Institute. Oakland, CA.
Leidy, R.A., G.S. Becker, B.N. Harvey. 2005. Historical distribution and current status of steelhead/rainbow trout
(Oncorhynchus mykiss) in streams of the San Francisco Estuary, Califormia. Center for Ecosystem Management and
Restoration, Oakland, CA.
Leidy, R.A., G.S. Becker, B.N. Harvey. 2005. Historical status of coho salmon in streams of the urbanized San Francisco
Estuary, California, California Department of Fish and Game.
Moyle, P.B. 2002. Inland fishes of California UC Press, Berkeley, CA.

http://ice.ucdavis.edu/aquadiv/fishcovs/fishmaps.html
National Marine Fisheries Service. 2010. Public Draft Recovery Plan for Central California Coast coho salmon
(Oncorhynchus kisutch) Evolutionarily Significant Unit. National Marine Fisheries Service, Southwest Region, Santa
Rosa, California.
RHJV (Riparian Habitat Joint Venture). 2004. The riparian bird conservation plan: a strategy for reversing the decline of
riparian associated birds in California. California Partners in Flight. http://www.prbo.org/calpif/pdfs/riparian_v-2.pdf
Robins, J.D. 2002. Stream Setback Technical Memo prepared for Napa County Conservation Development and
Planning Department. Jones & Stokes. Oakland, CA.
San Francisco Bay Regional Water Quality Control Board. July 2004. Local Government Riparian Buffers in the San
Francisco Bay Area. Oakland, CA.
San Francisco Bay Regional Water Quality Control Board, Staff Report, Evaluation of Water Quality Conditions for the
San Francisco Bay Region, Proposed Revisions to the 303(d) List, February 2009.

Page 74 of 76
Seavy, N.E., T. Gardali, G.H. Golet, F.T. Griggs, C.A.Howell, R. Kelsy, S.L. Small, J.H. Viers and J.F. Weigand. 2009.
Why Climate Change Makes Riparian Restoration More Important than Ever: Recommendations for Practice and
Research. Ecological Restoration, Vol 27, No.3.
Williams, Jack E.; Wood, Christopher A.; Dombeck, Michael P., Editors, Watershed Restoration: Principles and
Practices.

Page 75 of 76
Appendix A. Priority 1 and 2 Streams

(Anchor Watersheds and Essential Streams from Becker et al. 2007 and Core Areas from the Public Draft
Recovery Plan for Central California Coast coho salmon (Oncorhynchus kisutch) Evolutionarily Significant
Unit are in bold italics) Attached separately.
Appendix B. Essential Watersheds and Priority Stream Segments for Focused

Conservation Actions to Protect Native Fishes, San Francisco Estuary, California.
Robert Leidy, Ph.D., U.S. EPA, June 19, 2008 Attached separately.

Page 76 of 76

2010 Riparian/Fish Focus Team Report

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San Francisco Bay Area

Upland Habitat Goals

A Project of the Bay Area

Riparian/Fish Focus Team Report

Stuart B. Weiss, Ph.D., Nancy Schaefer and Ryan Branciforte

Project funded by:

California State Coastal Conservancy

The San Francisco Ba y Area Upland Habitat Goals

Appendix A. Priority 1 and 2 Streams....................................................................................................a separate document

Riparian/Fish Focus Team Report

RIPARIAN/FISH FOCUS TEAM REPORT

The report contains the following elements:

Riparian/Fish Focus Team Members

II. Role of the Riparian/Fish Focus Team

Riparian/Fish Focus Team Report

III. Riparian Defined

IV. Unique Role of Riparian Areas in Climate Change Adaptation

Riparian/Fish Focus Team Report

V. Riparian and Fish Resources in the San Francisco Bay Area

Table 1. Current Geographic Distribution and Population Status of Stream Fishes of

Riparian/Fish Focus Team Report

VI. Riparian/Fish Focus Team Methodology

Working Assumptions and Guiding Principles

Riparian/Fish Focus Team Report

Selecting Conservation Targets

Riparian/Fish Focus Team Report

Table 2. Fish Conservation Targets

Riparian/Fish Focus Team Report

Figure 1. Napa River Basin Fish Community (Koehler, 2007)

c. Stream Conservation Targets. As noted previously, the Riparian/Fish Focus Team

Riparian/Fish Focus Team Report

Riparian/Fish Focus Team Report

CEMAR Anchor CEMAR Anchor

Riparian/Fish Focus Team Report

Riparian/Fish Focus Team Report

Riparian/Fish Focus Team Report

Map 2. Priority 1 and 2 Coastal Streams

Riparian/Fish Focus Team Report

The following criteria were used to identify Priority 1 streams.

1) Alameda Creek tributaries below Calaveras and San Antonio Reservoirs

Riparian/Fish Focus Team Report

Riparian/Fish Focus Team Report

Map 3. Upland Habitat Goals Priority Streams

Riparian/Fish Focus Team Report

Table 5. San Francisco Bay Watersheds Ranked by Presence of Native Species

Anchor Watersheds and CalWater 2.2.1. Watersheds

Table 6. CEMAR vs. CalWater Watershed Levels

Calwater 2.2.1 Designation

Riparian/Fish Focus Team Report

Map 4. CEMAR vs. CalWater Watershed Levels

Riparian/Fish Focus Team Report

Compiling Available Data

Riparian/Fish Focus Team Report

Setting Conservation Goals

Map 5. San Francisco Bay Area Landscape Units

Riparian/Fish Focus Team Report

Map 6. CalWater 2.2.1 Hydrologic Areas

Table 7. Acreage Goals for Riparian Vegetation Types by Landscape Unit

Riparian/Fish Focus Team Report

The overarching goal of this Recovery Plan is to prevent the extinction of

Coho Recovery Target

Gazos Creek 279

a. Protection of all streams via fee or easement acquisition, cooperative agreement or

Riparian/Fish Focus Team Report