The San Francisco Bay Delta Model

Research Focus


In the proposed study, the new model will be applied to investigate the Delta's response to scenarios of climate change, including upstream hydrologic changes, downstream sea level rise, and changes in local meteorological influences such as heating and wind stress (4 GCM scenarios will be examined). Additionally, we will examine the effects of structural change, including proposed new freshwater conveyance infrastructure and breached levee scenarios (at minimum we expect to explore 1 configuration each for the infrastructure and breached levee scenarios by project end).

We plan to: 1) choose 2 representative historical years as “baseline” years (dry, wet), based on a combination of ranked river flow and hydrograph representativeness amongst the historical years, and 2) choose 2 future years with comparable flow rankings and hydrographs amongst the modeled future years). Historical “wet” and “dry” years will thus be comparable to future “wet” and “dry” years. Choosing specific years, as opposed to calculating “average” years as composites of many years, is necessary if the model is to be driven by episodically interconsistent boundary conditions (i.e. a stormy period that consistently affects river flows, sea level, and local meteorology, shown to be important by [14]). We see this approach as a starting point, and expect to adapt it as results progress. We plan to perform model runs with structural and climate change alone and in combination.

Computing resources at the UC San Diego Supercomputer Center will facilitate the completion of multiple 1-year scenarios from the hydrodynamic and other coupled models.


The future Bay-Delta system may undergo considerable change due to sea level rise, changing river flows, levee breaches, flooding, different water management strategies and wetland restoration projects. Future conditions (e.g. increased tidal prism) may change the sediment budget, resulting in altered turbidity levels and related ecological effects (e.g. on phytoplankton, fish) throughout the Bay-Delta system. Although there is a qualitative understanding of many of the sediment processes of the Delta, it is difficult to quantify the effects of changing conditions. Therefore there is a need for a model to quantitatively assess impacts of possible future scenarios on the Bay-Delta system, in particular the sediment related characteristics such as turbidity and morphology. The objectives of this task are to:

  1. use a model to better understand suspended sediment (SS) processes in the Bay-Delta;
  2. assess how SS dynamics may change under future scenarios; and
  3. explore implications for Delta geomorphology (due to the paucity of available validation data for the Delta and the need to first focus on characterizing and understanding the dominant sediment transport processes).

Analysis will focus on the Delta, but will include the Bay when necessary (e.g., propagation of water level and salinity from the ocean to the Delta). Climate and structural change scenarios will be run with the sediment model. The modeled sediment transport patterns in the Delta will be analyzed to increase understanding of sediment input, throughput and settlement/erosion in the Delta. DFLOW FM has an open source character so links can be made efficiently to other (e.g. phytoplankton) models used within the CASCaDE II framework via the Delft WAQ/ECO modules.


Phytoplankton biomass (PB) represents the dominant food supply to the pelagic foodweb supporting the Delta’s upper trophic levels such as fish and depends on the relative rates of algal growth, loss (e.g. to consumers), and transport. In turn, many other ecosystem components are influenced by phytoplankton growth and standing stock. We propose to address the questions:

  1. How are Delta PB and primary productivity (PP) directly and indirectly linked to water quality, hydrodynamic transport, and secondary producers?
  2. How will these relationships shift with changes in climate and Delta physical configuration?
  3. How can we improve on existing approaches for linking physical models with biological models?

Phytoplankton computations will be performed “offline”, using DFlow FM generated hydrodynamics (velocities, water surface elevations, turbulent diffusivities) and SSC. The partial differential equation to be solved for the evolution of PB includes terms representing advection, diffusion/dispersion, growth, and loss due to grazing. The spatial domain for this model will be Suisun Bay and the Delta, implementing seaward hydrodynamic boundary conditions derived from full Bay-Delta runs. Calculation of hydrodynamics, turbidity and phytoplankton “under one modeling roof” will significantly improve on our previous approach of specifying static turbidity maps from spatially coarse sampling.