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Salinity and Sediment Dynamics in San Francisco Estuary
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DSD-INT 2016 Salinity and Sediment dynamics in San Francisco Estuary - Elmilady

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Page 1: DSD-INT 2016 Salinity and Sediment dynamics in San Francisco Estuary - Elmilady

Salinity and Sediment Dynamics in San Francisco Estuary

Page 2: DSD-INT 2016 Salinity and Sediment dynamics in San Francisco Estuary - Elmilady

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

Page 3: DSD-INT 2016 Salinity and Sediment dynamics in San Francisco Estuary - Elmilady

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

Page 4: DSD-INT 2016 Salinity and Sediment dynamics in San Francisco Estuary - Elmilady

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

Page 5: DSD-INT 2016 Salinity and Sediment dynamics in San Francisco Estuary - Elmilady

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

Page 6: DSD-INT 2016 Salinity and Sediment dynamics in San Francisco Estuary - Elmilady

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

Page 7: DSD-INT 2016 Salinity and Sediment dynamics in San Francisco Estuary - Elmilady

1. Introduction

Problem Definition

San Pablo Bay

Suisun Bay Carquinez Strait

Delta

Saline Water

Fresh Water

Cross-Section

• Density Currents (Longitudinal Salinity Gradient)

Page 8: DSD-INT 2016 Salinity and Sediment dynamics in San Francisco Estuary - Elmilady

1. Introduction

Problem Definition

San Pablo Bay Suisun Bay Carquinez Strait

• Salinity Stratification

Page 9: DSD-INT 2016 Salinity and Sediment dynamics in San Francisco Estuary - Elmilady

1. Introduction

Research Question

San Pablo Bay Suisun Bay Carquinez Strait

• Salinity Stratification

How does the gravitational circulation and salinity stratification affect the

sediment exchange between San Pablo and Suisun Bay?

Page 10: DSD-INT 2016 Salinity and Sediment dynamics in San Francisco Estuary - Elmilady

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

Page 11: DSD-INT 2016 Salinity and Sediment dynamics in San Francisco Estuary - Elmilady

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

Page 12: DSD-INT 2016 Salinity and Sediment dynamics in San Francisco Estuary - Elmilady

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)

Page 13: DSD-INT 2016 Salinity and Sediment dynamics in San Francisco Estuary - Elmilady

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.

Page 14: DSD-INT 2016 Salinity and Sediment dynamics in San Francisco Estuary - Elmilady

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

Page 15: DSD-INT 2016 Salinity and Sediment dynamics in San Francisco Estuary - Elmilady

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)

Page 16: DSD-INT 2016 Salinity and Sediment dynamics in San Francisco Estuary - Elmilady

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)

Page 17: DSD-INT 2016 Salinity and Sediment dynamics in San Francisco Estuary - Elmilady

3. Calibration

Salinity Calibration

Target Diagram

2 2

N NTRMSD ubRMSD Bias

Page 18: DSD-INT 2016 Salinity and Sediment dynamics in San Francisco Estuary - Elmilady

3. Calibration

Salinity Calibration

Mo

de

lled

O

bse

rve

d

Salinity Transects

Dry Conditions Wet Conditions Moderate Conditions

Page 19: DSD-INT 2016 Salinity and Sediment dynamics in San Francisco Estuary - Elmilady

3. Calibration

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

Page 20: DSD-INT 2016 Salinity and Sediment dynamics in San Francisco Estuary - Elmilady

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.

Page 21: DSD-INT 2016 Salinity and Sediment dynamics in San Francisco Estuary - Elmilady

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

Page 22: DSD-INT 2016 Salinity and Sediment dynamics in San Francisco Estuary - Elmilady

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

Page 23: DSD-INT 2016 Salinity and Sediment dynamics in San Francisco Estuary - Elmilady

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

Page 24: DSD-INT 2016 Salinity and Sediment dynamics in San Francisco Estuary - Elmilady

4. Discussions and Analysis

San Pablo Bay Suisun Bay

Carquinez Cross-Section

Residual Flows

Page 25: DSD-INT 2016 Salinity and Sediment dynamics in San Francisco Estuary - Elmilady

San Pablo Bay Suisun Bay

No

Sal

init

y W

ith

Sal

init

y Tides

Gravitational Circulation

Tides

Flood Tide

Arrows to Scale

Landward Bottom Flow

Logarithmic Profile

4. Discussions and Analysis

Residual Flows

River Discharge

River Discharge

Page 26: DSD-INT 2016 Salinity and Sediment dynamics in San Francisco Estuary - Elmilady

San Pablo Bay Suisun Bay

No

Sal

init

y W

ith

Sal

init

y

River Discharge & Tides

Gravitational 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

Page 27: DSD-INT 2016 Salinity and Sediment dynamics in San Francisco Estuary - Elmilady

4. Discussion

No

Sal

init

y W

ith

Sal

init

y

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

Page 28: DSD-INT 2016 Salinity and Sediment dynamics in San Francisco Estuary - Elmilady

4. Discussion

Tracers (Tidal Cycle)

4. Discussions and Analysis

Time Step= 30 min

Wit

h S

alin

ity

No

Sal

init

y

San Pablo Bay Suisun Bay

Page 29: DSD-INT 2016 Salinity and Sediment dynamics in San Francisco Estuary - Elmilady

4. Discussion

No

Sal

init

y W

ith

Sal

init

y

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

Page 30: DSD-INT 2016 Salinity and Sediment dynamics in San Francisco Estuary - Elmilady

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

Page 31: DSD-INT 2016 Salinity and Sediment dynamics in San Francisco Estuary - Elmilady

4. Discussion 4. Discussions and Analysis

Residual Flows

Page 32: DSD-INT 2016 Salinity and Sediment dynamics in San Francisco Estuary - Elmilady

Interannual Variability

4. Discussion

San Pablo Bay Suisun Bay

Benicia Cross-Section

4. Discussions and Analysis

Page 33: DSD-INT 2016 Salinity and Sediment dynamics in San Francisco Estuary - Elmilady

Interannual Variability

4. Discussion

Total Cum. Suspended transport through BEN

25-Dec-2003 01-May-2004

Dry Wet Dry 760 Kt 86 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

Page 34: DSD-INT 2016 Salinity and Sediment dynamics in San Francisco Estuary - Elmilady

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 Flocs San 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 %

Page 35: DSD-INT 2016 Salinity and Sediment dynamics in San Francisco Estuary - Elmilady

Available Mass (kg/m2) 01-Oct-2003 00:00 Available 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

Page 36: DSD-INT 2016 Salinity and Sediment dynamics in San Francisco Estuary - Elmilady

Available Mass (kg/m2) 25-Dec-2003 00:00 Available 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

Page 37: DSD-INT 2016 Salinity and Sediment dynamics in San Francisco Estuary - Elmilady

4. Discussion

Sediment Budget (WY 2004)

4. Discussions and Analysis

Page 38: DSD-INT 2016 Salinity and Sediment dynamics in San Francisco Estuary - Elmilady

Sediment Budget (WY 2004)

4. Discussion

BEN

MAL CAR

BEN

MAL CAR

BEN

MAL CAR

• 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

Page 39: DSD-INT 2016 Salinity and Sediment dynamics in San Francisco Estuary - Elmilady

4. Discussion

BEN

MAL CAR

BEN

MAL CAR

• 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)

Page 40: DSD-INT 2016 Salinity and Sediment dynamics in San Francisco Estuary - Elmilady

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

Page 41: DSD-INT 2016 Salinity and Sediment dynamics in San Francisco Estuary - Elmilady

• 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

Page 42: DSD-INT 2016 Salinity and Sediment dynamics in San Francisco Estuary - Elmilady

• 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

Page 43: DSD-INT 2016 Salinity and Sediment dynamics in San Francisco Estuary - Elmilady

• 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

Page 44: DSD-INT 2016 Salinity and Sediment dynamics in San Francisco Estuary - Elmilady

Thank You

Page 45: DSD-INT 2016 Salinity and Sediment dynamics in San Francisco Estuary - Elmilady

Salinity and Sediment Dynamics in San Francisco Estuary