This document summarizes research linking hydrodynamic, water quality, sediment, and habitat suitability models to understand changes in the San Francisco Bay-Delta ecosystem under climate change and sea level rise scenarios. The researchers used the Delft3D modeling suite including Delft3D-FM for hydrodynamics and linked models for water quality, sediment, phytoplankton, and habitat suitability. The models were able to simulate historical conditions and predict increases in average salinity levels and shifts in the X2 position further upstream under higher sea level rise. The linked modeling approach allows for exploring how habitat may change for important species under different climate and infrastructure scenarios.

1. Rosanne Martyr-Koller1
J. Helly1, L. Lucas2, N. Knowles2, M. van der Wegen3
1 University of California – San Diego, La Jolla, CA, USA
2 United States Geological Survey, Menlo Park, CA, USA
3 UNESCO-IHE, Delft, Netherlands

2. Linking models to understand changes in the San
Francisco Bay-Delta Ecosystem
Climate: sea level rise, precipitation & resultant streamflows, direct
atmospheric forcing over the Delta
Physical Configuration: alternative conveyance, island flooding,
ecosystem restoration
Pollution/Water Quality: invasive species, contaminants, decreasing
turbidity

3. Delft3D-FM
DELWAQ
HABITAT

4. Linking models to understand changes in the
San Francisco Bay-Delta Ecosystem
*Hydrodynamic model description
*Hydrodynamics application: historical Bay-Delta hydrology, salinity
*Hydrodynamics application: sea level rise & salinity
*Coupled application: Hydrodynamics, sediment & phytoplankton
*Coupled application: Hydrodynamics, water quality & habitat
suitability
*Next steps: Climate, infrastructure scenarios

5. Linking models to understand changes in the
San Francisco Bay-Delta Ecosystem
*Software: Delft3D-FM
*Developed by Deltares, Inc.
*3D finite volume hydrodynamics
model
*Unstructured implementation of
Delft3D
*Includes salinity, temperature,
sediment, wind-wave capability

6. Linking models to understand changes in the
San Francisco Bay-Delta Ecosystem
*Tidally-driven
waterlevels at
Pacific Ocean
*Variable freshwater
flows
*Pumps
*Gates and dams
*Measurement-based
bathymetry
*10 vertical σ layers
Petaluma
Sonoma Napa
Sacramento
Mokelumne &
Cosumnes
American
San Joaquin
Yolo

7. Linking models to understand changes in the
San Francisco Bay-Delta Ecosystem
*Study period: 1 October, 2010 – 30 September, 2011 (WY2011)
Flow
stations
Salinity
stations
Waterlevel
stations

8. Linking models to understand changes in the
San Francisco Bay-Delta Ecosystem
Model Performance Statistics
R 0.97
RMSE 0.19m
Bias 0.004m
Skill 0.97

9. Linking models to understand changes in the
San Francisco Bay-Delta Ecosystem
Model Performance Statistics
R 0.94
RMSE 42.2 m3/s
Bias 3.35 m3/s
Skill 0.94

10. Linking models to understand changes in the
San Francisco Bay-Delta Ecosystem
Statistics Station
Average
Cruise
Average
R 0.91 0.98
RMSE 1.79 psu 1.95psu
Bias -0.47psu -0.39psu
Skill 0.91 0.98
WINTER
SUMMER

11. Linking models to understand changes in the
San Francisco Bay-Delta Ecosystem
Waterlevels Discharges
Model
bias high
Model
bias low
Obs. have
more
variance
Model has
more
variance

12. Linking models to understand changes in the
San Francisco Bay-Delta Ecosystem
Salinity Profile by Station Salinity Gradient by Cruise

13. *
Linking models to understand changes in the
San Francisco Bay-Delta Ecosystem

14. *Definition: the distance
between Golden Gate
Bridge and the daily 2psu
isohaline at the bottom of
the water column.
*Invented to track low
salinities.
Linking models to understand changes in the
San Francisco Bay-Delta Ecosystem
X2=47km X2=77km

15. *The position of X2 is managed at the State level as a water quality
metric.
(Federal Register, Vol. 59, Issue 4, January 6, 1994)
Linking models to understand changes in the
San Francisco Bay-Delta Ecosystem
*X2 must be positioned at
or downstream of these
locations for a required
number of days in the
spring (February-June).
*Freshwater from
reservoirs is released (if
available) to keep X2 at
these positions.

16. Linking models to understand changes in the
San Francisco Bay-Delta Ecosystem
*Study period: Water Year 2011(wet year) & Water Year 2012 (dry year)
*Modeled X2
showed good
agreement
with other
estimates.

17. Linking models to understand changes in the
San Francisco Bay-Delta Ecosystem
*Six 2-yr simulations: 1 base case (SLR=0cm), and 5 cases
using SLR amounts shown below.

18. Linking models to understand changes in the
San Francisco Bay-Delta Ecosystem
WY2011 WY2012

19. Linking models to understand changes in the
San Francisco Bay-Delta Ecosystem
SLR (cm)
Mean X2 (km)
WET YEAR DRY YEAR
2011 2012
0 68.2 75.6
33 70.7 76.8
67 72.5 78.0
100 73.9 79.8
134 75.1 81.4
167 76.5 82.9

20. Linking models to understand changes in the
San Francisco Bay-Delta Ecosystem
SLR (cm)
Mean X2 (km)
WET YEAR DRY YEAR
2011 2012
0 68.2 75.6
33 70.7 76.8
67 72.5 78.0
100 73.9 79.8
134 75.1 81.4
167 76.5 82.9
∆ Mean X2 (km)
WET
YEAR
DRY
YEAR
8.3 7.3

21. Linking models to understand changes in the
San Francisco Bay-Delta Ecosystem
SLR (cm)
Mean X2 (km)
WET YEAR DRY YEAR
2011 2012
0 68.2 75.6
33 70.7 76.8
67 72.5 78.0
100 73.9 79.8
134 75.1 81.4
167 76.5 82.9

22. Linking models to understand changes in the
San Francisco Bay-Delta Ecosystem
WET YEAR (2011)
February 1 – June 30
DRY YEAR (2012)
February 1 – June 30

23. Linking models to understand changes in the
San Francisco Bay-Delta Ecosystem
Regulatory Req. Sea Level Rise
Position Spring Req. 0cm 33cm 67cm 100cm 134cm 167cm
<64 133 days
<74 148 days
<81 150 days
WET
YEAR
(2011)
Regulatory Req. Sea Level Rise
Position Spring Req. 0cm 33cm 67cm 100cm 134cm 167cm
<64 33 days
<74 116 days
<81 150 days
DRY
YEAR
(2012)
Regulation Source: Federal Register,
Vol. 59, Issue 4, January 6, 1994;
FR Doc No.: 94-120

24. Linking models to understand changes in the
San Francisco Bay-Delta Ecosystem
For a desired X2, e.g.
55 km:
Current day needs ~
1500 m3/s of
freshwater.
SLR=167cm needs at
least twice that
amount of freshwater.

25. Linking models to understand changes in the
San Francisco Bay-Delta Ecosystem
Regulatory Req. Sea Level Rise
Position Spring Req. 0cm 33cm 67cm 100cm 134cm 167cm
<64 133 days
<74 148 days
<81 150 days
WET
YEAR
(2011)
Regulatory Req. Sea Level Rise
Position Spring Req. 0cm 33cm 67cm 100cm 134cm 167cm
<64 33 days
<74 116 days
<81 150 days
DRY
YEAR
(2012)
Regulation Source: Federal Register,
Vol. 59, Issue 4, January 6, 1994;
FR Doc No.: 94-120

26. *
Linking models to understand changes in the
San Francisco Bay-Delta Ecosystem

27. Linking models to understand changes in the
San Francisco Bay-Delta Ecosystem
Water depth Depth-averaged velocity
DFM-3D
DELWAQ -
Sediment
DELWAQ -
BLOOM
*DFM-3D can provide hydrodynamic information for every grid cell at
prescribed time intervals to be used as input to water quality model.

28. Suspended Sediment
Light Extinction Coeff.
Phytoplankton biomass
(Chl a)DFM Hydrodynamics
to DELWAQ Sediment
Module
Sediment Output
to BLOOM
Within
BLOOM
PRELIMINARY
DFM-3D
DELWAQ -
Sediment
DELWAQ -
BLOOM
Analysis:
L. Lucas

29. *
Linking models to understand changes in the
San Francisco Bay-Delta Ecosystem

30. Maps of
Environmental
Parameters
(measurement or
model)
Species Response
(HSI) Curves
(empirical
presence/absence)
Habitat
Suitability
Map
PRELIMINARY
©Deltares
DFM-3D DELWAQ HABITAT
©
Linking models to understand changes in the
San Francisco Bay-Delta Ecosystem

31. Water depth (model)
Salinity (model)
Temperature (meas.)
Proof of concept analysis:
J. Thompson
0
0.2
0.4
0.6
0.8
1
1.2
0 20 40
HabitatSuitability
Index Depth (m)
0
0.2
0.4
0.6
0.8
1
1.2
0 10 20 30
HabitatSuitability
Index
Temperature (C)
0
0.2
0.4
0.6
0.8
1
1.2
0 5 10
HabitatSuitability
Index
Salinity
HSI curves: DWR &
USGS Data, 1988-
2012
PRELIMINARY
Noel M. Burkhead - U.S.G.S.

32. Proof of concept analysis: J. ThompsonPRELIMINARY
Linking models to understand changes in the
San Francisco Bay-Delta Ecosystem

33. Salinity (meas.)
Temperature (meas.)
Secchi (meas.)
Photo: Peterson USFWS
Preliminary analysis: L. Brown, M. Wulff
0
0.2
0.4
0.6
0.8
1
1.2
0 10 20 30 40
HSI
Salinity (ppt)
0
0.2
0.4
0.6
0.8
1
1.2
0 10 20 30
HSI
Temp (C)
0
0.2
0.4
0.6
0.8
1
1.2
0 1 2 3
HSI
Secchi Depth (m)
Input maps: 2014 FMWT
HSI curves: IEP-
CDFG FMWT data,
1967-present

34. Preliminary analysis: L. Brown, M. Wulff
20142011
Linking models to understand changes in the
San Francisco Bay-Delta Ecosystem

35. *
Linking models to understand changes in the
San Francisco Bay-Delta Ecosystem

36. • Inclusion of temperature in Delft3D-FM
• Climate scenarios
• Near-century, end-of-century cases
• Low, medium, & high increases in temperature
• Wet, dry cases
• Alternate conveyance, flooded islands scenarios
• Explore how habitat for species of interest might
move/shrink/increase as a function of different major
drivers of change
• Habitat analyses for:
• multiple fish, 2 bivalves
• compare seasons, hydrologic regimes, etc.

37. *SFEI-led Nutrient Management Strategy
*Deltares-initiated SFB-D “Community Model”
http://www.d3d-baydelta.org/

38. Linking models to understand changes in the
San Francisco Bay-Delta Ecosystem
*CASCaDE Team Lisa Lucas, Noah Knowles, John Helly, Mick van der Wegen,
Fernanda Achete, Bruce Jaffe, Theresa Fregoso, Wim Kimmerer, Jan Thompson,
Larry Brown
*Deltares, Inc.
*USGS  Jim Cloern, Tara Schraga, Charles Martin, Erica Nejad
*Funding for this research is provided by the Delta Stewardship Council/Delta Science
Program and USGS Priority Ecosystems Science