The Nutrient Management Strategy (NMS) program has developed numerical models to simulate the hydrodynamics and biogeochemical processes in San Francisco Bay. The NMS uses these models to study nutrient cycling and the effects of nutrients on water quality in the Bay. This report presents a progress update on numerical model development and capabilities, with an emphasis on work carried out from 2023 to 2026.

Updates to the hydrodynamic model processes included:

• improvements to temperature simulation, 
• simulating additional water years, and
• refining the model grid. 

The hydrodynamic model was evaluated for its ability to accurately predict water level, velocity, salinity, and temperature. The evaluation showed that the model reproduces all four variables well over the eleven years simulated.

Updates to the biogeochemical model processes included: 

• incorporating light extinction coefficients that are more spatially and temporally resolved,
• updating the observation-based ocean boundary conditions, 
• updating the initial conditions for the water column and sediment,
• refining phytoplankton mortality modeling to reduce dependence on poorly-parameterized grazers, 
• incorporating a new sediment denitrification formulation, 
• simplifying particle exchange between the water column and Bay-floor to be setting and remineralization only,
• analyzing the impacts of different dissolved oxygen saturation and reaeration formulas.

As these updates were incorporated, the biogeochemical model output was calibrated and evaluated through comparisons with data collected by channel cruises, moored sensors, shoal-mapping cruises and satellites. Calibration broadly focused on improving model predictions of three metrics: primary production, dissolved inorganic nitrogen, and dissolved oxygen. The evaluation showed that the model performed reasonably well in capturing seasonal trends across all three metrics. Specific improvements to the model included a better representation of the processes that drive the late summer nitrogen drawdown.

Sensitivity analyses were conducted to test the relative impact of adjusting certain processes in the model. Those analyses are presented for assessment. Among potential future improvements, the team highlights the need to resolve overestimates of primary production and dissolved oxygen during summer months. Improving phosphorous and silica cycling will also be a valuable next step.