Groundwater Model Methods

Groundwater heads (heights) were modeled along the California coast using the USGS
modular groundwater flow software MODFLOW. The model includes water inputs in the form
of recharge through the tops of model cells (simulating infiltration from precipitation), and
outputs to surface drainage features (streams, lakes etc.) and to the ocean. Tops of model cells
were set to the ground surface based on topographic data. To determine steady-state groundwater
levels in model cells, groundwater was allowed to flow through model cells until the model
reached equilibrium for the chosen set of parameter values (marine boundary condition,
horizontal and vertical hydraulic conductivity, sea level). Steady-state conditions were evaluated
for a range of parameter values to bracket the range of likely conditions and groundwater
responses for present-day and future sea-level rise conditions.

Spatial domain and topographic/bathymetric data

The coast of California was separated into five regions corresponding to published
continuous and seamless 2 m LIDAR topographic-bathymetric digital elevation models (DEMs)
in the NAVD88 vertical datum (Fig. 1). Input data and resulting models for all regions except
Southern California (SoCA; Point Conception to the Mexican border) used a NAD 1983(CSRS
2007) UTM zone 10N (EPSG: 3717) coordinate system. SoCA data used zone 11N (EPSG:
3718). All DEMs except for the San Francisco Bay area were limited primarily to areas with
elevations less than ~10 m above mean sea level and thus extended no more than a few
kilometers inland from the present-day coastline. In the San Francisco Bay region, model
domains were extended farther inland to encompass most watershed divides that would drain to
the bay or outer coast. To allow emergent groundwater to fill surface depressions and create
standing water bodies, non-marine (above 0m NAVD88) areas of DEMs were preprocessed by
filling closed topographic depressions. The DEMs were then transformed to the internal
groundwater model coordinate system and interpolated to the model cell centers using bilinear
interpolation.
Figure 1. Model regions delineated by available DEMs

Marine boundary condition

Mean higher-high water (MHHW) and local mean sea level (LMSL) elevations relative
to NAVD88 were calculated using NOAAs VDATUM vertical transformation database and
software (https://www.vdatum.noaa.gov/). A vertical value of 0 m NAVD88 was defined along
CA coastal locations defined after O’Reilly et al. (2016), and transformed to MHHW or LMSL
to obtain the water level surface above NAVD88. MHHW/LMSL levels were interpolated to
groundwater model grid cells using the nearest neighboring MHHW/LMSL points. For each sea
level rise (SLR) scenario, the magnitude of SLR for each model was added to the present-day
MHHW/LMSL level to define which model cells were inundated by marine waters.
Long-term mean surface salinity data was obtained from globally gridded data of the
NODC World Atlas Annual Long Term Mean Salinity
(https://www.esrl.noaa.gov/psd/data/gridded/data.nodc.woa94.html) The data represent long
term annual means derived from data for years 1900-1992 using all observations available (in-
situ and satellite). Gridded data are at 0.25 degree resolution (~28 km x 28 km). Data exist at
various depths, with the shallowest being at the surface, 10 m, and 20 m. A comparison was done
to investigate the overall difference between surface and 10 m depth salinity and was found to be
minimal with a difference of <0.02 ppt along most of the coast except near San Francisco Bay.
These gridded data were interpolated to the same coastal locations used for defining sea levels
[O’Reilly et al., 2016]. For San Francisco Bay, additional observed salinity data between 1968-
2015 were used to constrain the groundwater flow models [Schraga and Cloern, 2017]. The
density of the coastal waters were calculated using the Thermodynamic Equation of Seawater -
2010 [Feistel, 2008] by using the mean water temperature and position of the coastal locations to
calculate the absolute salinity from the practical salinity and location data, the conservative
temperature from in-situ temperatures, and finally the density from the conservative temperature
and absolute salinity, all under the approximation of water at atmospheric pressure. The water
densities were then normalized to a water temperature of 13 degrees C, the approximate average
annual coastal water temperature. These salinity data were interpolated to the groundwater model
grid cells using the nearest neighboring salinity points and applied only to marine cells identified
using the MHHW or LMSL levels as appropriate.

Recharge
Groundwater recharge rates were bilinearly interpolated to the model grids from the mean
annual average effective recharge reconstructions for 2000-2013 (Reitz et al., 2017b, 2017a).

Groundwater flow model

The USGS modular groundwater flow software MODFLOW (MODFLOW -2005 version
1.11.00) was used to simulate the water table and groundwater flow for coastal CA settings. The
Python package FloPy was used to develop the model inputs and read the model outputs.
Groundwater model solution domains were manually drawn to divide the California coast into 57
smaller, overlapping areas that resembled buffered watershed boundaries. A shapefile containing
each domain as a separate feature was then used to construct the MODFLOW model domain
using the smallest bounding rectangle of each domain feature.
Each of the 57 MODFLOW models was run with the same suite of boundary conditions
and hydrogeologic properties. Coastal water depths were assigned using the MHHW or LMSL
level added to the amount of sea-level rise in each model scenario, and these water levels were
set as the tidal and marine boundary condition as constant heads. For active, non-marine cells, a
combined recharge-drain (RCH, DRN packages) condition along the top of the cells allowed
flexible, though highly nonlinear, solution of the water table elevation (Sanford, 2002). To
stabilize the nonlinearity of solving for groundwater flow and the water table elevation across the
model, a Newton-Raphson solver (NWT) was used. All models were comprised of one model
layer that extended from the surface topography to -50 m NAVD88 with a horizontal cell size of
10 m by 10 m. A homogeneous hydraulic conductivity was set for this layer in the horizontal
directions with a vertical hydraulic conductivity set to be one-tenth of that value. To test the
effects of hydraulic conductivity (and therefore transmissivity) on the model outputs, each
modeled sea level rise scenario was modeled with three unique horizontal hydraulic
conductivities: 0.1, 1.0, and 10 m/day. All MODFLOW models were run in steady-state mode.

Acknowledgements
NODC_WOA94 salinity data were provided by the NOAA/OAR/ESRL PSD, Boulder, Colorado,
USA, from their Web site at https://www.esrl.noaa.gov/psd/

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