Salmonberry River Temperature Monitoring 1994-2018

STEP Project Report

Executive Summary

Summer water temperature monitoring has been conducted since 1994 in the
Salmonberry River (Nehalem basin) under a STEP project. Temperature data were
gathered from 1994 through 1997, in 2004 (with limited data), and 2007 through
2018. Current plans are to continue monitoring annually.

In the most recent report, “Salmonberry River Temperature Monitoring 1994-
2015”, I analyzed temperature trends in the Salmonberry, and reported a trend of
increasing summer average daily high temperatures, at a rate of .056° C ± .041° C
per year over the 22-year period. With three more years of data, the annual rate of
increase now stands at .068° C ± .04° C (p=.002).

Another trend analyzed in the previous report is an increase in days above the
DEQ/EPA “Core Cold Water Habitat” standard of 16° C (60.8° F), measured as a
moving 7-day average of daily maximum temperature. The prior report points out
that a possible implication of registering increasingly more days above 16° C is that
the warming might be occurring farther up in the watershed, effectively reducing
suitable habitat for species dependent on cooler water. This report shows the trend
is continuing, and includes mapping to demonstrate the known upstream extent of
violations of the core habitat standard.

Optimal habitat for cold-water dependent species is shrinking. To help track the
extent, additional monitoring sites farther upstream will be established in 2019.



Prepared by Ian Fergusson
April 2019

1. Introduction

This is an abbreviated report; its main focus is to examine possible trends. Methods,
materials, general discussions, and project history have all been presented under
various reports (2007, 2008, 2009, 2010, 2011, and 2015). Those reports can be
viewed by searching the ODFW Data Clearinghouse for the keyword “Salmonberry”
at the following link:
https://nrimp.dfw.state.or.us/DataClearinghouse/default.aspx?p=1 .

Original data files are kept on a personal Macintosh computer, backed up with a
cloud-based service. A data file is also uploaded to the Data Clearinghouse site.

Support for this project has been through ODFW STEP (Salmon Trout Enhancement
Program), with grants for equipment purchases through STEP-STAC (Salmon Trout
Advisory Committee) mini-grants. The ODFW North Coast office oversees the
project. The project involves a significant volunteer effort, with donations of time,
use of personal vehicles, data maintenance, and data analysis.

2. Statistics and Data Presentation

The software used for data analysis is “R version 3.2.4” (R Core Team, 2016. R: A
language and environment for statistical computing. R Foundation for Statistical
Computing, Vienna, Austria. URL http://www.R-project.org/. Charts and outline
maps were produced using the “ggplot2” package for R (H. Wickham. ggplot2:
Elegant Graphics for Data Analysis. Springer-Verlag New York, 2009). Microsoft
Excel Version 16.2 for Macintosh is used for data storage, data analysis and
presentation of tables.

2. Monitor Locations

Currently, we monitor 7 main stem sites and 7 tributary sites in the Salmonberry
watershed (Nehalem River basin). See map, Figure 1. Prior to 2009, we monitored
10 sites. In 2009 we added mainstem sites at the mouth, below the South Fork,
above the North Fork, and one tributary site (Bathtub Creek).

Data loggers are placed following standard protocols (e.g., Dunham et al., 2005).
Turbulent, well-mixed sites are selected. Placement is as close to the thalweg as
possible. Data loggers are shielded from direct sunlight by white PVC housings. They
are anchored with a rock and duct tape, and secured with cable to a log, root wad, or
to a second rock. A plastic plant nursery tag, inscribed “Temperature monitor
attached-please do not disturb” with permanent marker, is attached to the anchor
end of the cable (away from the data logger). Due to the risk of vandalism, care is
taken to conceal the locations; flagging is placed in the vicinity but not right at the
site. Detailed notes, photos, and GPS waypoints are used to help relocate the loggers
in the fall.

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Figure 1. Salmonberry River watershed, showing temperature monitor locations. Port of Tillamook
RR in red.

3. Equipment Changes

From 1994-1997 and again in 2004, ODFW provided Onset Hobo® temperature
loggers, with resolution of 0.1⁰ C. These were programmed by ODFW to log
temperatures 10 times per day.

Beginning in 2007, we decided to begin annual temperature monitoring, and ODFW
purchased 10 NexSens® model 1921G loggers for use by the project team, with
resolution of 0.5⁰ C and accuracy of ±1⁰ C. Late in 2008, the project was awarded a
STAC mini-grant, and we purchased 10 additional NexSens® model 1921G loggers.
These were deployed at additional sites beginning in 2009. A drawback of the
NexSens loggers is limited memory, which does not allow for logging at 30-minute
intervals as recommended by DEQ; we had to log every 2 hours in order to be able
to store data for the entire summer deployment period.

In 2016 we began using 15 Onset Hobo TidbiT V2® data loggers, purchased with an
additional STAC mini-grant. These allow logging every 30 minutes, and have a
resolution of 0.02°C and accuracy of ±0.21°C at the temperatures normally
encountered in stream habitat.

One result of the equipment changes is that more frequent logging increases the
probability of capturing the actual high and low temperatures (Dunham et al.,
2005). Less frequent logging can result in understatement of key metrics such as the

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DEQ/EPA core cold water habitat standard based on the seven-day average daily
maximum (7DADM). See Section 4.B for a discussion of adjustments made in an
attempt to compensate for differences in measurement frequency.

4. Trend Analysis

A. Rising Temperatures

This section is an update of the trend analysis done in 2015, adding three more
years of data. As of 2018 we have 17 summers of data over a span of 22 years.

Besides the gaps in years, within measured years there are sites that have no data.
This makes a watershed-wide average impractical without extensive estimates of
missing values. Reporting results for all individual stations is cumbersome. I
compromised by using the average of three upper to middle main stem stations that
have values for all monitored years except 2004: main stem above Pennoyer Creek,
main stem below Wolf Creek, and main stem below North Fork. Because of their
locations, these main stem stations also reflect temperatures of waters contributed
by Pennoyer Creek, Wolf Creek, Kinney Creek, Belding Creek, and the North Fork
(see map, Figure 1 for reference). Thus, the entire upper watershed contributes to
these values.

In order to make year-to-year comparisons as meaningful as possible, I used a date
range for each summer with the latest common start date (June 20) and the earliest
common end date (Sep 5) for all years. The daily high temperature was averaged
over the entire period.

The updated linear regression (Figure 2) continues to indicate an increasing trend
in daily maximum temperatures (slope = .068, p = .002, Pearson’s r = .702, 95% CI
[.028, 0.107]). The annual rate of increase over the period is .068° C ± .04° C.

Note: The gap in data between 1997 and 2007 raises the question of whether a
linear regression over the entire time period 1997-2018 is appropriate. If in those
unknown years the temperatures were extremely high or low compared to the
known years, that would render the slope and other characteristics of the
regression line invalid. I approached that problem in the last report by developing
an equation that allows an approximation of the missing values. The equation uses
the very high correspondence between known Salmonberry maximum
temperatures and the maximum daily air temperatures recorded at the NOAA
Vernonia 2 weather station (GHCND:USC00358884). I updated the air to water
conversion formula using three more years of data (2016-18) and recalculated the
estimated water temperature values for the missing years. None of them changed
from the prior calculation. Figure 2 displays the estimated points, which are there
for illustration only; they are not used in the calculation of the water temperature
trend.

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 Salmonberry R Summer Avg Highs, with estimated points
16 ●
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15 ● ●
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14 ● ● ●
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13 ●
12
11
Avg High, °C

10
9
8
7
6
5
4
3
2
1
0
1994 1996 1998 2000 2002 2004 2006 2008 2010 2012 2014 2016 2018

Figure 2. Salmonberry River water temperatures with linear regression trend line and 95%
confidence band. Hollow circles indicate where water temperature data are missing. The missing
values were not used in calculating the trend line. See text for explanation.

B. Increasing Trend of Exceedances of EPA Core Cold Water Standard

Oregon DEQ has designated the Salmonberry main stem and tributaries as subject to
the “core cold-water habitat” standard. This standard (16⁰ C), is defined as the
upper limit for core juvenile salmonid rearing habitat (except for bull trout). The
pertinent wording in the Oregon Administrative Rules (340-041-0028 (4) (b)) is
“The seven-day-average maximum temperature of a stream identified as having core
cold water habitat use…may not exceed 16.0 degrees Celsius (60.8 degrees
Fahrenheit).”

To determine whether the watershed as a whole is showing a trend, I used the
original 10 sites as the sample. Each of those sites has 0 or only 1 instance of a
missed year, except for 2004, when only three sites provided valid data due to
stream dewatering. 2004 was excluded from the analysis. As with the average daily
high temperature analysis, I used the period from June 20 – September 5 to ensure a
consistent measure of total days (10 sites X 78 days=780 days in each season).
Where data were missing for the summer, the missing value was filled in with an
estimate based on comparisons with other sites/years. All sites prior to 2016 were
then adjusted as necessary to compensate for less frequent recording to better
evaluate changes in number of days above 16° C over time. Note that the
adjustments add days for observations prior to 2016. Without the adjustments, an
exaggerated increase over time could result.

5
To make the adjustment for less frequent recording, I started with the datasets
generated during 2016-18, where temperatures were recorded every 30 minutes. I
created new datasets from them that used only the data recorded every two hours
starting at midnight each day, which was the regime programmed for the NexSens
loggers 2008-2015. I evaluated the differences between the two sets to arrive at a
protocol for adjusting the summarized results.

For results prior to 2016, if at least one day was recorded where the 7DADM
exceeded 16° C, I adjusted upward using the left hand columns in Table 1. Where the
original count was 0 days, I adjusted according to the average daily maximum, using
the right hand columns in Table 1.

Days Original Avg Days
Original Count Added Daily High Added
1-10 days 1 < 14.9 0
11-20 days 4 14.9 - 15 4
21-30 days 3 15.1 - 15.2 5
31-40 days 2 15.3 - 15.4 3
> 40 days 0 15.5 - 15.6 2
> 15.6 0
Table 1. Factors used to adjust days above 16° C, for years where temperature readings were taken
every two hours.

The adjusted results are shown in Table 2 and Figure 3.

Table 2. Number of days (adjusted; see text) with an exceedance of DEQ Core Cold Water Habitat
Standard, 1994-1997 and 2007-2018. Total exceedance site-days (Total) are divided by 780 total
site-days in each year to arrive at the proportion.

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 0.5

0.4
●

●
Proportion

0.3

●
●
0.2 ●
●

●
●
●
0.1 ●
●
●
● ●
● ●

0.0
1994 1995 1996 1997 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 2018



Figure 3. Proportion of site-days where exceedance of the DEQ “Core Cold Water Habitat Standard”
occurred, with fitted loess (locally weighted least squares regression) curve and 95% confidence
band. Explanation in text.


The results reflect the rise in average temperatures, with an increasing trend
strongly influenced by temperatures recorded in the last five years. This trend can
be interpreted as a sign of shrinking habitat. An increase in total site-days in excess
of 16⁰ C can mean that potential temperature impairment not only lasts longer at a
given site, but also affects sites not previously affected. Thus, there are fewer stream
miles available with suitable temperatures. This shrinking habitat is illustrated in
the following two maps (Figures 4 and 5), which display the minimum and
maximum upstream extents of cold-water habitat violations recorded since 2009.
2009 was the first year in which we deployed monitors in the main stem just below
the South Fork and just above the North Fork.

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 .
R
em

●
al

Salm
eh

o nber North Fork

ry R.
N

●
●

Belfort ●

●
Cr. ●
● ●
●
Pennoyer
●
●
● ●
Cr.
Bathtub ●
Kinney
South Fork Cr. Cr.
Wolf Cr.

0 1 2 3 4 5
Kilometers


Figure 4. Salmonberry River watershed, showing monitor sites (hollow circles) and extent of
violations of EPA/DEQ Core Cold Water Habitat standard (red line). This pattern occurred in 2010
and 2011 and represents the minimum extent recorded since 2009 (note the 4-day violation in Wolf
Creek in 2011 is shown here; no violation occurred in Wolf Creek in 2010).


Results in recent years (Figure 5) suggest a change in monitor sites is needed in
order to better establish the upstream extent of cold-water habitat violations in the
future. The plan for summer 2019 is to monitor three new sites: the main stem just
above Wolf Creek, the North Fork about 3.7 km (2.3 mi) above the current site, and
Wolf Creek about 2.9 km (1.8 mi) above the current site. Proposed sites are shown
in Figure 5.

We have 15 TidbiT V2 loggers, 14 of which are deployed. The spare logger will be
deployed, and the loggers currently at the Salmonberry mouth and in Bathtub Creek
will be moved.

8
 .
R
em

●
al

Salm
eh

onber North Fork

ry R.
N

●
●
Belfort ●
Cr. ●●
● ●● Pennoyer
●● Cr.
Bathtub ● ● ●
Kinney
South Fork Cr. Cr.
Wolf Cr.

0 1 2 3 4 5
Kilometers

Figure 5. Salmonberry River watershed, showing extent of violations of EPA/DEQ Core Cold Water
Habitat standard (red line). This pattern occurred in 2009, 2014, 2015, 2016, 2017, and 2018, and
represents the maximum extent recorded since 2009 (note the 3-day violation in the South Fork in
2018 is shown here; this was the only violation we have recorded in the South Fork). Triangles show
3 proposed new sites; hollow circles with X show 2 current sites that will be discontinued; plain
circles show existing sites that will continue to be monitored.

C. Trends in Certain Tributaries

Several past reports have considered changes in water temperatures in tributaries
that were scoured by debris flows in the February 1996 and December 2007 major
storm events. Two tributaries, Pennoyer Creek and Belfort Creek, did not see any
major scouring in either event. Wolf Creek, Kinney Creek, and Bathtub Creek were
affected along much of their lengths.

Pennoyer Creek serves as a control in this analysis. The other tributaries are viewed
by how much, and in what direction, their temperatures differ from Pennoyer Creek.
This method theoretically corrects for climate impacts, since climate effects over
such a small area should affect Pennoyer Creek just as much as the others. In reality,
Pennoyer Creek may achieve some buffering from climate effects largely due to the
presence of Cochran Pond, approximately 2.6 km (1.6 mi) above the creek’s mouth.
Maxted et al. (2005) found significant increases in downstream temperatures
resulting from in-line ponds; however, the spillways in that study discharged water
from the pond surfaces, while the Cochran Pond’s discharge is at the base of the
earthen dam. If temperature stratification occurs in Cochran Pond, that could result
in cooler downstream temperatures. Another possible buffering effect would occur
if the pond mimics a large beaver pond. Beaver ponds have been shown to enhance
hyporheic flow and connection between surface and subsurface flows (Weber et al.,

9
2017), and if that effect occurs in Pennoyer Creek, it would tend to lead to cooler
and more stable temperatures below the pond.

The average daily range of temperatures in Pennoyer Creek over the most recent
three years is less than at any other monitored site (Table 3), suggesting a buffering
effect is occurring.

Mean Daily Mean Daily
Site Range, Maximum,
Pennoyer Cr. 1.46 12.8
Main stem above Pennoyer 1.61 13.5
Belfort Cr. 1.62 13.4
Kinney Cr. 1.62 14.8
Bathtub Cr. 1.64 13.5
Main stem below North Fk. 1.79 15.1
Wolf Cr. 2.14 15.0
North Fork 2.22 14.6
Main stem below Wolf 2.23 14.8
Main stem above North Fk. 2.42 15.4
South Fork 2.64 14.2
Main stem below South Fk. 2.81 16.0
main stem below Belfort 3.38 17.2
Main stem at mouth 3.85 18.5

Table 3. Mean daily temperature ranges, and mean daily maximum, at monitored Salmonberry sites,
2016-18. Sorted in ascending order of mean daily range.

The following plots (Figure 6) show the differences in average daily maximum from
Pennoyer Creek for seven monitor sites (six tributaries and the uppermost main
stem site). Each point is the average of the 61 daily highs recorded during July and
August of each year where a record exists for that site. The horizontal line at 0
represents Pennoyer Creek.

The plots in Figure 6 demonstrate some interesting patterns over time. In general,
temperatures are increasing relative to Pennoyer Creek at most sites. Kinney Creek
and Wolf Creek display an obvious reaction to the major rain-on-snow event of
February 1996, in which both streams were scoured by debris torrents.
Temperatures have been elevated since then, without showing any significant sign
of trending back down to the 1994-95 relationships. The major flood event of
December 2007 also resulted in debris torrents in both streams, which may be a
contributing factor in the prolonged warming. The lack of a difference in Wolf Creek
in 2004 is probably the result of the creek going subterranean in several spots and
emerging just above the monitor site; Kinney Creek and the upper main stem dried
completely during 2004 at the monitor sites.

10


Bathtub Creek was also scoured by debris flows in both major events. Although no
temperature data exist for Bathtub Creek prior to the 2007 debris torrent,
temperatures there have been trending down (relative to Pennoyer Creek) since
that event.

Belfort Creek (where there were no major debris flows in 1996 or 2007) cycles
within less than 1°C of Pennoyer Creek; the last 5 years have all been warmer than
Pennoyer. It remains to be seen whether this is a developing trend.


Bathtub Cr. Belfort Cr. Kinney Cr.
4
3 ●
2 ● ● ● ● ● ● ● ●
● ● ●
● ● ● ● ● ●
1 ●
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● ●
0
● ●
●
● ●
●
● ● ●
● ● ● ●
−1 ● ● ●
−2
−3
−4
Difference From Pennoyer, °C

1994
1995
1996
1997
2004
2007
2008
2009
2010
2011
2012
2013
2014
2015
2016
2017
2018

1994
1995
1996
1997
2004
2007
2008
2009
2010
2011
2012
2013
2014
2015
2016
2017
2018

1994
1995
1996
1997
2004
2007
2008
2009
2010
2011
2012
2013
2014
2015
2016
2017
2018
North Fk South Fk Upper MS
4
3
2 ● ● ● ● ● ●
● ● ● ● ● ● ● ● ●
1 ● ● ● ● ● ● ● ● ●
● ● ● ● ● ● ● ● ● ● ● ●
0 ● ● ● ● ● ●
● ● ● ● ●
−1
−2
−3
−4
1994
1995
1996
1997
2004
2007
2008
2009
2010
2011
2012
2013
2014
2015
2016
2017
2018

1994
1995
1996
1997
2004
2007
2008
2009
2010
2011
2012
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2014
2015
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2017
2018

1994
1995
1996
1997
2004
2007
2008
2009
2010
2011
2012
2013
2014
2015
2016
2017
2018
Wolf Cr.
4
3 ● ● ●
2 ● ● ● ● ● ● ●
● ● ●
1 ● ●
0 ●
−1
−2
−3
−4
1994
1995
1996
1997
2004
2007
2008
2009
2010
2011
2012
2013
2014
2015
2016
2017
2018

Figure 6. Mean daily high temperature differences from Pennoyer Creek, for 1 main stem site and 6
tributary sites.

5. Cooling Effect of North Fork

Table 3, while aimed at displaying the narrow range of daily temperatures in
Pennoyer Creek, also points out the cooling effect of the North Fork. The site just
above the North Fork has a daily range of 2.42⁰ C and average daily high of 15.4⁰ C.
The site just below the North Fork has a daily range of 1.79⁰ C and average daily
high of 15.1⁰ C.

11
The North Fork is the major spawning tributary in the Salmonberry system;
steelhead redd counts indicate that more than half the Salmonberry run has
spawned in the North Fork since the December 2007 flood that reshaped the
Salmonberry main stem. 34% of spawning occurred in the North Fork from 1994 –
2007; 58% thereafter (STEP spawning survey data,
https://nrimp.dfw.state.or.us/DataClearinghouse/default.aspx?p=1 . ).

6. Discussion

Even with the limitations of the data (entirely missing 1998-2003; most stations
missing 2004; entirely missing 2005-2006; differences in logger sensitivity and
recording frequency), there is strong evidence of increasing temperatures in the
Salmonberry.

There is a strong correlation (Pearson’s r=.894) between Salmonberry water
temperatures and Vernonia air temperatures, indicating that area climate variations
are having the greatest impact on Salmonberry water temperatures. The adjusted r2
value (.785) suggests that 79% of the variation in Salmonberry water temperatures
can be explained by area climate variations, with Vernonia air temperatures as a
surrogate.

Many interacting factors can cause variations in stream temperature. Solar
radiation, substrate type, canopy cover and topographic shading, hyporheic flow, re-
radiation, evaporation and convection at the air-water interface, stream surface
area, stream length, stream order, pool characteristics, discharge, gradient, channel
roughness, air temperature, relative humidity, and wind speed are among the
variables considered important (Brown, 1972; Beschta and Taylor, 1988; Zwieniecki
and Newton, 1999; Bartholow, 2000; Johnson and Jones, 2000; Johnson, 2004).

Precipitation during the summer can affect minimum stream flows, which may also
affect temperatures. Oregon coastal streams do not rely on a melting snow pack for
maintaining water supply. Modest decreases in summer precipitation and modest
increases in winter precipitation are projected effects of climate change in Western
Oregon (Mote et al., 2019). In addition, recent research (Perry and Jones, 2016)
continues to shed light on the complex relationships between timber harvest and
stream flows, which may also be a factor in the Salmonberry watershed with
increased harvest of relatively mature Douglas Fir planted after the Tillamook
Burns.

Regardless of causes, there is a developing problem in the Salmonberry watershed
that may already be having biological effects. For species requiring cooler water,
such as juvenile salmon and steelhead, optimal summer habitat is shrinking. Even
with the possibility of increased food supply for juvenile salmonids due to warmer
water, McCullough et al. (2001) stated that disease becomes a significant mortality
factor in temperatures above optimum levels, and that water temperatures in
salmon-rearing reaches must be managed in order to provide the greatest salmonid

12
population production capacity, ensuring a full range of temperatures: very cold
headwaters, cold midreaches, and cold/cool lower reaches.

Citations:

Bartholow, J. 2000. Estimating cumulative effects of clearcutting on stream
temperatures. Rivers 7(4), 284-297.

Beschta, R, and R.L. Taylor. 1988. Stream temperature increases and land use in a
forested Oregon watershed. Water Res. Bull. 24: 19-25.

Brown, G. 1972. An improved temperature prediction model for small streams.
Research Report WRRI-16, Water Resources Research Institute, Oregon State
University, Corvallis, OR. 20 p.

Dunham, J., G. Chandler, B. Rieman, and D. Martin. 2005. Measuring stream
temperature with digital data loggers: a user’s guide. Gen. Tech. Rep. RMRS-GTR-
150WWW. Fort Collins, CO: U.S. Department of Agriculture, Forest Service, Rocky
Mountain Research Station. 15 p.

Johnson, S. 2004. Factors influencing stream temperatures in small streams:
substrate effects and a shading experiment. Can. J. Fish. Aquat. Sci. 61: 913-923.

Johnson, S. and J. Jones. 2000. Stream temperature responses to forest harvest and
debris flows in western Cascades, Oregon. Can. J. Fish. Aquat. Sci. 57: 30-39.

Maxted, J.R., C.H. McCready, and M.R. Scarsbrook. 2005. Effects of small ponds on
stream water quality and macroinvertebrate communities. New Zealand Journal of
Marine and Freshwater Research 39:1069-1084.

McCullough, D., S.Spalding, D.Sturdevant, and M.Hicks. 2001. EPA Issue Paper 5.
Summary of technical literature examining the physiological effects of temperature
on salmonids. US Environmental Protection Agency EPA-910-D-01-005. 114 p.

Mote, P.W., J. Abatzoglou, K.D. Dello, K. Hegewisch, and D.E. Rupp, 2019: Fourth
Oregon Climate Assessment Report. Oregon Climate Change Research Institute.
occri.net/ocar4.

Perry, T.D. and Jones, J.A.. 2016. Summer streamflow deficits from regenerating
Douglas-fir forest in the Pacific Northwest, USA, Ecohydrology, doi: 10.1002/
eco.1790

Weber N, Bouwes N, Pollock MM, Volk C, Wheaton JM, Wathen G, et al. (2017)
Alteration of stream temperature by natural and artificial beaver dams. PLoS ONE
12(5): e0176313. https://doi.org/10.1371/journal.pone.0176313

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Zwieniecki, M. and M. Newton. 1999. Influence of streamside cover and stream
features on temperature trends in forested streams of western Oregon. West. J. Appl.
For. 14: 106-112

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