Presentation by Hesham Elmilady (UNESCO-IHE) at the Delft3D User Days, during Delft Software Days 2016. Wednesday 2 November 2016, Delft.

1. Salinity and Sediment Dynamics in
San Francisco Estuary

2. Master of Science Thesis
By
Hesham M. Elmilady
UNESCO-IHE, Department of Water Science and Engineering
Coastal Engineering and Port Development
Supervisors
Prof.dr.ir. Dano Roelvink (UNESCO-IHE & Deltares)
Dr. Thijs van Kessel (Deltares)
Mentor
Dr. Mick van der Wegen (UNESCO-IHE & Deltares)
Examination Committee
Prof.dr.ir. Dano Roelvink
Dr. Thijs van Kessel
Dr. Mick van der Wegen
2nd November 2016
Salinity and Sediment Dynamics in San Francisco Estuary

3. 1. Introduction
San Francisco Estuary
Problem Definition and Research Question
2. Numerical Model
Model Domain
Forcing Conditions
3. Calibration
Salinity Calibration
Hydrodynamic Calibration
Temperature Calibration
Suspended Sediment Concentration Calibration
4. Discussions and Analysis
Residual Flows
Tracers
Interannual Variability
Sediment Budget
5. Conclusions and Recommendations
Presentation Contents

4. 1. Introduction
San Francisco Estuary
San Francisco Estuary (Google Earth)
• The largest estuary on the west coast
of the U.S.
• Its enormous watershed drains
approximately 40% of California’s
area (Kimmerer 2004).
• Only link to the Pacific Ocean is
through the Golden Gate Bridge.
• Commonly referred to as the Bay-
Delta system which includes the
Sacramento-San Joaquin Delta and
the San Francisco Bay.
• 3 main Sub-embayments:
- South Bay
- Central Bay
- North Bay
Pacific Ocean
Golden Gate
Sacramento-San Joaquin Delta
South Bay
Central Bay
Northern Bay
Map Area

5. 1. Introduction
Northern San Francisco Bay
Northern San Francisco Bay (Google Earth)
• The Northern San Francisco Bay
comprises:
1) San Pablo Bay
2) Suisun Bay
3) Carquinez Strait
• Carquinez Strait is the only
connection between San Pablo and
Suisun Bay
San Pablo Bay
Suisun Bay
Carquinez Strait

6. 1. Introduction
Northern San Francisco Bay Bathymetry
1) San Pablo Bay:
• Northern and Southern shoals dissected
by a deep shipping channel
• Connected to the Central Bay through
San Pablo Strait.
2) Carquinez Strait:
• Narrow cross-section (1000 m)
• Deep Nature (max ~35 m)
• Steep Slopes
• Complicated Geometry (Multiple Bends)
• Rocky banks
3) Suisun Bay:
• Shoals dissected by two deep channels
(Northern and Southern Channel)
• Connected to the delta through a narrow
cross section at Point Mallard
Northern San Francisco Bay
San Pablo Bay
Suisun Bay
Carquinez Strait
Delta
Southern Channel
Northern Channel
Sacramento River
San Joaquin River

7. 1. Introduction
Problem Definition
San Pablo Bay
Suisun BayCarquinez Strait
Delta
Saline Water
Fresh Water
Cross-Section
• Density Currents (Longitudinal Salinity Gradient)

8. 1. Introduction
Problem Definition
San Pablo Bay Suisun BayCarquinez Strait
• Salinity Stratification

9. 1. Introduction
Research Question
San Pablo Bay Suisun BayCarquinez Strait
• Salinity Stratification
How does the gravitational circulation and salinity stratification affect the
sediment exchange between San Pablo and Suisun Bay?

10. 1. Introduction
San Francisco Estuary
Problem Definition and Research Question
2. Numerical Model
Model Domain
Forcing Conditions
3. Calibration
Salinity Calibration
Hydrodynamic Calibration
Temperature Calibration
Suspended Sediment Concentration Calibration
4. Discussions and Analysis
Residual Flows
Tracers
Interannual Variability
Sediment Budget
5. Conclusions and Recommendations
Presentation Contents

11. 2. Numerical Model
Model Domain
• 3D process based numerical
model developed with the
Delft3D software.
• Curvilinear structured mesh
with variable grid resolution.
• Covers the entire Northern
San Francisco Bay and a
section of the delta with its
two main river branches.
• Vertical layering
- 15 sigma layers
- Z-layers (1m resolution)
• Online coupling of the flow
model with wave model
(SWAN).
The geographical coverage of the Model Domain (Google Earth)
Suisun Bay
Sacramento River
San Joaquin River
Napa River
Delta

12. 2. Numerical Model
Boundary Data
Richmond:
• Water Levels
• Temperature
• Salinity
Napa:
• Discharge
• Temperature
• SSC
Rio Vista:
• Discharge
• Temperature
• SSC
Jersey:
• Discharge
• Temperature
• SSC
Wind Field
Model Domain and Boundary Definition (Google Earth)
Legend:
• (Field Measurements)
• (Correlations developed
with measurements
form different Water
Years)
• (Data obtained from
Numerical Models)

13. 2. Numerical Model
Richmond:
• Water Levels
• Temperature
• Salinity
Napa:
• Discharge
• Temperature
• SSC
Rio Vista:
• Discharge
• Temperature
• SSC
Jersey:
• Discharge
• Temperature
• SSC
Wind Field
Model Domain and Boundary Definition (Google Earth)
Forcing Conditions
1) Tidal Forcing represented
by the water levels
specified at Richmond
Boundary.
2) Fresh water input
represented by the river
discharge at Napa, Rio-
Vista and Jersey.
3) Wind represented by the
spatially and temporally
varying wind field across
the model domain.

14. 1. Introduction
San Francisco Estuary
Problem Definition and Research Question
2. Numerical Model
Model Domain
Forcing Conditions
3. Calibration
Salinity Calibration
Hydrodynamic Calibration
Temperature Calibration
Suspended Sediment Concentration Calibration
4. Discussions and Analysis
Residual Flows
Tracers
Interannual Variability
Sediment Budget
5. Conclusions and Recommendations
Presentation Contents

15. 3. Calibration
Monitoring Stations (Field Measurements)
Monitoring Stations in Northern San Francisco Bay (Google Earth)
• Data from WY 2004
• Eight monitoring stations spread
along the Northern San Francisco
Bay (USGS & NOAA)
• Six stations has two sensors
(Upper and Lower sensor) that
provides an instantaneous (15-
minute interval) time series of:
1) Salinity
2) Temperature
3) Suspended Sediment
Concentration (SSC)

16. 3. Calibration
Salinity Calibration
Benicia
Wet Conditions Dry Conditions
Upper Sensor Salinity (psu)Upper Sensor Salinity (psu)
Lower Sensor Salinity (psu)Lower Sensor Salinity (psu)

17. 3. Calibration
Salinity Calibration
Target Diagram
2 2
N NTRMSD ubRMSD Bias 

18. 3. Calibration
Salinity Calibration
ModelledObserved
Salinity Transects
Dry Conditions Wet ConditionsModerate Conditions

19. 3. Calibration
Hydro-Dynamic Calibration
1) Water Levels at 3 monitoring points. 2) Currents from 2 ADCPs

20. 3. Calibration
Temperature Calibration
• The model was subjected to water temperature
calibration using data from 6 monitoring stations.
• Water temperature has a small contribution to the
water density and it is included in the UNESCO
formulation for the water density computations in the
Delft3D.
• The results of the temperature calibration showed
good model performance in predicting the temperature
field.

21. 3. Calibration
SSC Calibration
Sediment Fraction τcr,e (Pa) M (kg m-2 s-1) ws (mm s-1) D50 (µm)
Silt 0.1 2.5×10-5 0.1
Flocculated clay and silt (Flocs) 0.2 5×10-5
1.5
Sand 400
Flocs
Silt
• Three sediment fractions was applied over the model domain
Sand
• Initial bed composition generated using the methodology defined
in van der Wegen et al. (2010).
Sediment Fractions

22. 3. Calibration
SSC Calibration
• SSC calibration results shows a good performance in predicting the SSC field.
• The results at the upper sensors are better than that for the lower sensor which is mainly attributed to the freshly
deposited sediment layer and the use of the sigma layers (Artificial Mixing).
Carquinez Benicia

23. 1. Introduction
San Francisco Estuary
Problem Definition and Research Question
2. Numerical Model
Model Domain
Forcing Conditions
3. Calibration
Salinity Calibration
Hydrodynamic Calibration
Temperature Calibration
Suspended Sediment Concentration Calibration
4. Discussions and Analysis
Residual Flows
Tracers
Interannual Variability
Sediment Budget
5. Conclusions and Recommendations
Presentation Contents

24. 4. Discussions and Analysis
San Pablo Bay Suisun Bay
Carquinez Cross-Section
Residual Flows

25. San Pablo Bay Suisun Bay
NoSalinityWithSalinity
Tides
Gravitational
Circulation
Tides
Flood Tide
Arrows to Scale
Landward Bottom Flow
Logarithmic Profile
4. Discussions and Analysis
Residual Flows
River Discharge
River Discharge

26. San Pablo Bay Suisun Bay
NoSalinityWithSalinity
River Discharge
& TidesGravitational
Circulation
Residual Flows Ebb Tide
Arrows to Scale
Seaward Near Surface Flow
Logarithmic Profile
SIPS (Strain-induced periodic stratification) Mechanism
4. Discussions and Analysis
River Discharge
& Tides

27. 4. Discussion
NoSalinityWithSalinity
Residual Flows
Flood Tide Ebb Tide
+ =
+ =
Tidal Cycle
Residual Flow
• Seaward near surface
residual flow.
• Landward bottom
residual flow.
• Seaward residual flow
over the entire water
column
4. Discussions and Analysis

28. 4. Discussion
Tracers (Tidal Cycle)
4. Discussions and Analysis
Time Step= 30 min
WithSalinityNoSalinity
San Pablo Bay Suisun Bay

29. 4. Discussion
NoSalinityWithSalinity
Residual Flows
Flood Tide Ebb Tide
+ =
+ =
Tidal Cycle
Residual Flow
Dry Conditions
• Seaward near surface residual flow
• Bottom landward residual flow
• Seaward residual flow
4. Discussions and Analysis
• Seaward residual flow
Wet Conditions
• Seaward residual flow

30. 4. Discussion
Residual Flows
Salinity (psu)
4. Discussions and Analysis
San Pablo Strait San Pablo Bay Carquinez Strait Suisun Bay
SSC San Pablo Bay Sediment
SSC Boundary Sediment

31. 4. Discussion4. Discussions and Analysis
Residual Flows

32. Interannual Variability
4. Discussion
San Pablo Bay Suisun Bay
Benicia Cross-Section
4. Discussions and Analysis

33. Interannual Variability
4. Discussion
Total Cum. Suspended transport through BEN
25-Dec-2003 01-May-2004
Dry Wet Dry
760 Kt86 days 126 days 153 days
All Fractions
• Water year 2004 is a wet WY is divided to:
65% Dry season
35% Wet season
• Without Salinity, Suisun Bay exports
sediment during the whole WY.
• With Salinity, Suisun Bay:
Dry Season: Equilibrium or Import
Wet Season: Export
• The total difference between both
simulations is 760 Kt, divided:
80% Dry season
20% Wet season
• The effect of the gravitational circulation
and salinity stratification is more
pronounced in the dry season than that for
the wet season.
4. Discussions and Analysis
A
Import
Export

34. Interannual Variability
4. Discussion
San Pablo Bay sediment
• San Pablo Bay sediment is imported
to Suisun Bay for both cases during
all of the WY except for a very short
period that corresponds to the highest
peak discharges.
San Pablo FlocsSan Pablo Silt
4. Discussions and Analysis
• The system quickly recovers from the
effect of the peak river discharge and
turns to import after a short period.
• The rate of sediment import from San
Pablo Bay to Suisun Bay decreases
during the wet season.
• The effect of the gravitational
circulation and salinity stratification is
more pronounced for San Pablo Bay
Silt than that for the Flocs.
Export Export≈66 %
≈30 %

35. Available Mass (kg/m2) 01-Oct-2003 00:00Available Mass (kg/m2) 01-Oct-2003 00:00
San Pablo Bay Sediment
No Salinity With Salinity
4. Discussion
Start of Simulation
Only Shoals Shoals and Deep Channel
Interannual Variability
4. Discussions and Analysis
Bathymetry

36. Available Mass (kg/m2) 25-Dec-2003 00:00Available Mass (kg/m2) 25-Dec-2003 00:00
No Salinity With Salinity
4. Discussion
Bathymetry
End of First Dry Period
Only Shoals Shoals and Deep Channel
Interannual Variability
4. Discussions and Analysis
San Pablo Bay Sediment

37. 4. Discussion
Sediment Budget (WY 2004)
4. Discussions and Analysis

38. Sediment Budget (WY 2004)
4. Discussion
BEN
MALCAR
BEN
MALCAR
BEN
MALCAR
• Suisun Bay is depositional during WY 2004.
• Wet season (Erosional):
Import from the delta
Export to Carquinez Strait and San Pablo Bay
• Dry season (Depositional):
Import from the delta, Carquinez Strait and San Pablo Bay
4. Discussions and Analysis

39. 4. Discussion
BEN
MALCAR
BEN
MALCAR
• The sediment import at the model boundaries is approximately the same for both cases (with and without salinity).
• The effect of the gravitational circulation and salinity stratification starts at Mallard and increases when going seaward.
• Suisun Bay turns from being depositional ( 20 Kt ) to erosional ( 680 kt).
• Gravitational circulation and salinity stratification not only imports sediment to Suisun Bay during the dry season but also
decreases the seaward sediment export from Suisun Bay during the wet season.
Sediment Budget (WY 2004)
4. Discussions and Analysis
(With Salinity)

40. 1. Introduction
San Francisco Estuary
Problem Definition and Research Question
2. Numerical Model
Model Domain
Forcing Conditions
3. Calibration
Salinity Calibration
Hydrodynamic Calibration
Temperature Calibration
Suspended Sediment Concentration Calibration
4. Discussions and Analysis
Residual Flows
Tracers
Interannual Variability
Sediment Budget
5. Conclusions and Recommendations
Presentation Contents

41. • A 3D modelling approach is critical for the Northern Bay as the 3D process related to the density currents
and salinity stratification has a significant effect on the sediment dynamics during the whole water year.
• The gravitational circulation and salinity stratification alters the flow patterns through Carquinez Strait:
During the dry season: During the wet season:
- Seaward near surface residual flow - Seaward residual flow over the entire water
- Landward bottom residual flow. column
• The salinity stratification and gravitational circulation is responsible for both:
A) Importing sediment to Suisun Bay during the dry season.
B) Decreasing the sediment export from Suisun Bay during the wet season.
• The effect of the gravitational circulation and salinity stratification in Carquinez Strait is more pronounced:
A) During the dry season than that for the wet season.
B) For the finest cohesive sediment (Silt) than that for coarser cohesive sediment (Flocs).
5. Conclusions and Recommendations
Conclusions

42. • Suisun Bay is deposition during WY 2004:
A) Depositional during the dry period
B) Erosional during the wet period
• The sediment exchange between San Pablo and Suisun Bay can occur through either:
- Deep Channel (Gravitational Circulation and Salinity Stratification)
- Relatively shallow areas (Hydrodynamic conditions – Tidal and Riverine Forcing)
5. Conclusions and Recommendations
Conclusions

43. • Distinguishing between the effect of the gravitational circulation and salinity stratification by
evaluating the longitudinal salinity gradient and using the horizontal Richardson number
(Monismith et al. 1996; Stacey et al. 2001).
• Distinguishing between the advective, dispersive and stokes drift flux.
• Applying the use of the Delft 3D flexible mesh to capture the system’s complicated geometry.
• The application of the fluffy layers (van Kessel et al. 2010 ) to simulate the effect of the freshly
deposited sediment layer.
• Studying the effect of the wind generated waves on the sediment transport.
• Assessing the effect of the seal-level rise on the Northern Bay.
Recommendations and Future Work
5. Conclusions and Recommendations
To be Considered for investigation
Currently under investigation

44. Thank You

45. Salinity and Sediment Dynamics in
San Francisco Estuary