Presentation by Sienna White, Stanford University, USA, at the Delft3D - User Days (Day 4: Water quality and ecology), during Delft Software Days - Edition 2019. Thursday, 14 November 2019, Delft.

1. Using D-Water Quality & D-Flow FM to
model cohesive sediment transport in
San Francisco Bay Sienna White
siennaw@stanford.edu
Oliver Fringer
fringer@stanford.edu

2. Past masters theses that contributed to this project:
Gostic, M., 2018. Sediment pathways in San Francisco South Bay. Master’s thesis, TU Delft.
van Kempen, O., 2017. Sediment pathways in San Francisco South Bay. Master’s thesis, TU Delft.
Pubben, S., 2017. 3D mixing patterns in San Francisco South Bay. Master’s thesis, TU Delft.

3. San Francisco Bay

4. North Bay
San Pablo Bay
South Bay
Central Bay
Suisun Bay

5. gold
greed
850
million m3
of sand
Moftakhari, H., Jay, D. A., Talke, S. A., Schoellhamer, D. H., 2015. Estimation of historic flows
and sediment loads to San Francisco Bay , 1849–2011. Journal of Hydrology 529, 1247–1261.

6. Shirzaei, Manoochehr, and Roland Bürgmann. "Global climate change and local land subsidence
exacerbate inundation risk to the San Francisco Bay Area." Science advances 4, no. 3 (2018).
Why does sediment matter?
muddy water = cleaner water
contaminant tracking
flood protection

7. Jaffe, B., Foxgrover, A. C., 2006. A history of intertidal flat area in South San
Francisco Bay , California: 1858 to 2005. Tech. rep., US Geological Survey.

8. 1. How does sediment influx from local tributaries in South Bay
affect sediment transport in South Bay?
2. How do wind waves affect sediment transport in South Bay?
3. What is the net sediment flux at the Dumbarton Bridge during
water year 2013?
Research Questions:

9. Hydraulic characteristics of
San Francisco Bay
Tides: standing waves in South
Bay, strong M2 & K1 constituents
at the Golden Gate Bridge

10. Hydraulic characteristics of
San Francisco Bay
Byxbee Park, Palo Alto ~2pm
Waves: fetch-limited in SFB.
Parameterized in our model
via bottom shear stress
(Grant & Madsen 1979).

11. [fun] cohesive sediment properties
Sediment characteristics of
San Francisco Bay

12. Bed Consolidation

13. Flocculation

14. Footage courtesy of Daniel Livsey, USGS

15. [fun] cohesive sediment properties!

16. Boundary Forcings
Initial Condition
Hydrodynamics
D-Water Quality
DELWAQ Model
DELWAQ Input
+ switch on relevant
processes, define
parameters.

17. Boundary Forcings
Initial Condition
Hydrodynamics
D-Water Quality
DELWAQ
DELWAQ Input
Freshwater predicted with
hydrologic model, SSC
calculated with rating curves
Equilibrium bed
composition estimated
using averaged bottom
shear stress
D-Flow FM model

18. Model Results

20. Bever, A. J., MacWilliams, M. L., 2013. Simulating sediment transport processes in San Pablo Bay using coupled hydrodynamic, wave, and sediment
transport models. Marine Geology 345, 235–253.

22. SSC transport
during a tidal
cycle

23. Deposition &
erosion in the
fluff layer over
a tidal cycle

24. Define transects for
cumulative sediment
flux calculation @ the
Dumbarton Bridge

26. USGS Preliminary Data
Livsey, DN, Downing-Kunz, M, and Schoellhamer, D. (in review) The effect of flocculation on suspended-sediment flux
measurements in tidally affected systems.
Cumulative Sediment Flux at the Dumbarton Bridge

27. Effect of minor tributaries on sediment flux

28. Effect of waves on sediment flux

29. Answering our research questions:
1. How does sediment influx from local tributaries in South Bay affect
sediment transport in South Bay?
a. Minor tributaries increase sediment import at the Dumbarton into South Bay on the
order of 16% (likely a minimum).
2. How do wind waves affect affect sediment transport in South Bay?
a. Waves decrease SSC variance in South Bay by damping deposition during ebb and
slack tide, and such, increase residual sediment flux into South San Francisco Bay.
3. What is the net sediment flux at the Dumbarton Bridge during water
year 2013?
a. The net flux is positive → 525.7 ktons moving landward over October 2012 - October
2013.

30. Open source: accessible to a broader
scientific community
Can calculate sediment budgets + flux
for transects difficult to access in situ.
Strengths
Validation difficult/weak with
sparse data availability
No mass exchange between
sediment classes
No spatial/temporal variation in
sediment properties and dynamics
Weaknesses
Applicable sediment model for SSC
signals on spring-neap time scales
No feedback between
hydrodynamics +
morphodynamics
Quick runtime: ~ 4 days of wall-clock
time to run 5 months on a 64-bit
16 core AMD Opteron processor
(clockspeed 2.3 Ghz)

31. 1. Minor tributaries increase sediment import at the Dumbarton into South Bay on the order
of 16% (likely a minimum).
2. Waves decrease SSC variance in South Bay by damping deposition during ebb and slack
tide and thus increase residual sediment flux into South San Francisco Bay.
3. The net flux is positive → 525.7 ktons moving landward over October 2012 - October
2013.
Acknowledgements:
Joe Adelson at Stanford; Daniel Livsey and Maureen Downing-Kunz at USGS; Emma Nuss, Rusty
Holleman, Allie King, and Zhenlin Zhang at the San Francisco Estuary Institute; Mick van der Wegen
all the TU Delft students who worked on developing this model: Michelle Gostic, Oxana van Kempen,
Fernanda Achete, and Silvia Pubben; and Arjen Markus at Deltares.
Thank you & questions !