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Representative
Projects
San Francisco Bay-Delta Model to Evaluate Pelagic Organism
Decline
The motivation for this study is the observed decline of
delta smelt and other pelagic organisms of the upper San Francisco Estuary.
Three general factors identified to explain lower pelagic productivity are 1)
toxic effects; 2) exotic species effects; and 3) water project effects
(Action Plan 2007). For each of these factors the location and movement of
delta smelt are likely to be critical for understanding the reasons for the
pelagic organism decline (POD) and the efficacy of any actions taken to
sustain pelagic fish populations.
 The UnTRIM Bay-Delta model developed for the Delta Risk
Management Strategy (DRMS) project was extended to include the entire
Sacramento-San Joaquin Delta. The
results from the 3-D UnTRIM model of the San Francisco Bay-Delta are being
used with a Particle Tracking Model (PTM) developed by Dr. Edward Gross. The particle tracking simulations are being
compared to observed delta smelt distributions to test fish behavior
hypotheses.
The UnTRIM Bay-Delta model developed for this project is
the first three-dimensional hydrodynamic model extending from the Pacific
Ocean through the entire Sacramento-San Joaquin Delta. This model is suitable for detailed studies
of Delta hydrodynamics, including but not limited to:
• Investigating
the potential impacts of sea level rise on salinity intrusion into the Delta;
• Predicting
salt entrainment into the Delta resulting from Delta levee failure(s);
• Assessing
the suitability alternative conveyance strategies for Delta water supply.
• Quantifying
potential impacts of alternative conveyance strategies on Delta hydrodynamics
and water quality.
Delta Risk Management Strategy Hydrodynamic Modeling
The Sacramento-San Joaquin Delta is a critical resource to
the state of California because the Delta is a source of drinking water for
roughly 2 out of 3 Californians. However, the 2,800 km2 of islands
in the Delta region are at risk of inundation from levee failures. These
deeply subsided islands are protected by levees typically 4 to 5 meters high
which are, in most cases, not engineered levees and are constructed partially
with peat and other weak and compressible soils. The Delta Risk Management Strategy
(DRMS) has been funded by the California Department of Water Resources to
“look at sustainability of the Delta, and … assess major risks to
the Delta resources from floods, seepage, subsidence, and earthquakes”
(DWR). Part of this effort involves the application of hydrodynamic models to
estimate the effect of levee failures on salinity in the Delta. Levee
failures in the Delta generally result in increased salinity as islands flood
and brackish water from Suisun Bay is entrained into the Delta. Increased
salinity can result in exceedence of water quality
objectives for drinking water causing interruption of water exports,
resulting in a large economic impact.
 Several hydrodynamic and water quality simulation tools are
applied in the DRMS project, ranging from a tidally-averaged
advection-dispersion model, which can perform a decade of salinity
projections in less than 1 minute of computation time, to the sophisticated
and computationally intensive three-dimensional model, UnTRIM. The UnTRIM and TRIM3D models were used to
develop dispersion coefficients for the 1-D Water Analysis Module (WAM), and
to inform uncertainty analysis for results derived from one- and
two-dimensional simulations. Working
with URS Corporation and RMA, specific applications were developed
to evaluate the three-dimensional effects resulting from channel-island
exchange flow following levee failure, evaluating the three-dimensional
effects which impact the effectiveness of flushing flows aimed at pushing
salt our of the Delta, and investigating the three-dimensional component of
potential salinity intrusion into the Delta resulting from sea level rise.
More Information about DRMS UnTRIM San Francisco Bay-Delta
Model (1.25 MB)
Lower Deer Creek Restoration & Flood Management
Feasibility Study
Deer Creek drains the west slope of the southern Cascades flowing
westward through bedrock canyons and joining the Sacramento River near the
town of Vina in Tehama County, CA. It is one of only three streams in the
Central Valley still supporting wild populations of the federally threatened
spring run Chinook salmon. A federally
constructed flood control project on lower Deer Creek has led to degraded
habitat in Deer Creek, and multiple levee failures during large floods. A
variety of flood management alternatives are being considered for lower Deer
Creek.
 A detailed hydrodynamic model for lower Deer Creek was
developed using an unstructured three-dimensional hydrodynamic model,
UnTRIM. Simulations were made of the
1997 flood on Lower Deer Creek, during which levee failure occurred. The simulations reproduced the large-scale
features of the 1997 flood event based on the DWR conceptual model and were
validated against flood observation data.
The results demonstrate the important features influencing
flow on the lower Deer Creek floodplain and are being used to help guide the
planning, design, and implementation of future restoration and flood
management strategies. This work
provided the baseline for a larger CALFED Feasibility project which has
included collaboration with CH2M Hill, McBain &
Trush, Mussetter Engineering, Inc, and the Deer Creek Watershed Conservancy.
More Information about Deer Creek (5.5 MB)
Hamilton Wetlands Restoration Project
Aquatic Transfer Facility Technical Study
The Hamilton Wetlands Restoration Project is a joint
undertaking by the U.S. Army Corps of Engineers and the California Coastal Conservancy
to restore 650 acres of tidal marsh bordering San Pablo Bay. The restoration effort is expected to make
use of more than 5.4 million m3 of dredged materials to raise the elevation
of subsided wetlands. The placement of
an Aquatic Transfer Facility (ATF) in San Pablo Bay is being considered by
the U.S. Army Corps of Engineers to serve as a temporary holding site for
dredge sediments before they are transferred to the Hamilton Wetlands
restoration site.
A three-dimensional unstructured grid hydrodynamic model of
San Francisco Bay was developed to support this restoration project using the
UnTRIM model. The model was  calibrated and validated using two independent data
sets. The calibrated and validated
model results established a baseline hydrodynamic condition for comparison to
conditions after an ATF is introduced.
An ATF was introduced by adding an excavated pit to the existing
bathymetry. The suitability of ATF configurations
was evaluated by using the predicted near bed velocities and shear stress to
evaluate the potential for sediment resuspension
from the ATF for each scenario.
This work was conducted as part of a the Technical Study of
the Hamilton Wetlands Restoration Project Aquatic ATF through collaboration
between Dr. MacWilliams, the U.S.G.S, the U.S. Army Corps of Engineers San
Francisco District, Sea Engineering,
Inc., and Coastal & Marine Environments (CME). Other aspects of the study included
sediment sampling and sediment transport analysis, instrumentation and
monitoring of currents and suspended sediment, and an analysis of historical
geomorphic change in San Pablo Bay.
More Information about Hamilton ATF Project (1.8 MB)
South San Francisco Bay
Salt Pond Restoration
Worked with Dr. Edward Gross and the Schaaf & Wheeler
project team on the San Francisco Bay
Salt Pond Restoration Initial Stewardship Plan. The salt pond project represents one of the
largest land transfers and land planning projects in the history of the San
Francisco Bay Area. The overall land transfer includes 16,100 acres. The
Initial Stewardship Plan  (ISP) area encompasses approximately
15,300 acres. The purpose of the ISP project has been to plan for the
cessation of salt production and to maintain the biological and physical
conditions within the south bay salt ponds in the interim period between the
cessation of salt-making activities and the implementation of a long term
restoration plan. Contributions to
this effort included three-dimensional simulations of tidal sloughs,
including Alviso Slough, Coyote Creek, and Alameda Flood Control
Channel. Implemented sensitivity
analysis of model parameters to provide estimates of uncertainty on model
results. Developed suite of graphical visualization tools to analyze results
from salt pond models and three-dimensional salinity simulations. Studied localized changes in velocity,
salinity, tidal elevation, and tidal prism resulting from the implementation
of project alternatives. Conducted
detailed modeling and analysis of impact of levee breaches on local
hydrodynamics.
The Initial Stewardship Plan was
approved by the San Francisco Regional Water Quality Control Board on March
17, 2004. ISP releases from the ponds
began in April 2004; additional releases occurred in the summer of 2004 and
in March 2005 and the Island Ponds were restored to tidal action in March
2006. The ISP continues to serve as a
management guideline for pond operations while the long-term restoration plan
is being developed.
More Information about Tidal Slough Simulations (1.5 MB)
Three-Dimensional Hydrodynamic Modeling of the San
Francisco Estuary: Toward Understanding the Mechanisms Relating Flow to
Abundance of Estuarine Biota
 The purpose of this modeling effort is to investigate the
potential mechanisms underlying the relationships of fish abundance to flow
(“fish-X2”), which form the basis for the current
salinity standard for the San Francisco estuary. The project is funded by the CALFED
Bay-Delta Program and is a collaborative effort with Dr. Edward Gross and Wim Kimmerer. A
three-dimensional hydrodynamic model was applied to San Francisco Bay, San
Pablo Bay, Suisun Bay and the western Sacramento-San Joaquin Delta to improve
understanding of salinity transport mechanisms. The model was calibrated and validated the
model against current meter and salinity data including velocity profile and
salinity transect data. Simulation
results were used to investigate tidal time scale hydrodynamics including the
formation and destruction of vertical stratification. Residual velocities and
salt transport mechanisms in Carquinez strait and
Suisun Bay were analyzed.
More Information about San Francisco Bay Simulations (1.8 MB)
Abundance or survival of several estuarine biological
populations in the San Francisco Estuary is positively related to freshwater
flow. These relationships have been described in terms of X2, the
location of the 2 psu bottom salinity. Predictions of X2 from the San
Francisco Bay simulations were compared with X2 values computed
from regression equations currently used for management operations and with X2
estimated from USGS channel salinity observations.
More Information about Simulating Salt Intrusion and X2
Calculation (0.7 MB)
Evaluation of Shear Stresses in Incised and Compound
Channels
Modeled flow velocities and shear stresses in incised and
restored channel using 1-D and 3-D models.
Incised and restored channel geometries were developed based on pre-
and post-project conditions on Tassajara Creek,
CA. Evaluated the effectiveness of
compound channels for reducing bed shear stresses and flow velocities during
high flows and the capacity of 1-D and 3-D models to quantify these
reductions. This work demonstrated
that compound channels can be effective at reducing channel bed shear
stresses, but concluded that one-dimensional hydraulic models were not suitable
for assessing these reductions.
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