Biogeochemical simulation of San Francisco Bay using an unstructured-grid model

San Francisco Bay (SFB) is characterized as a high nutrient low chlorophyll ecosystem under strong river and ocean influences. To investigate the phytoplankton and nutrient dynamics, an unstructured-grid physical-biological model system (SCHISM+CoSiNE) was used to study the seasonal and interannual variabilities. The model captured SFB variability from 2005 to 2014 with high statistical performance and skill. The results show that the high chlorophyll concentration in South Bay is persistent in warm months, while chlorophyll in North Bay has strong interannual variation. Nutrient concentration is higher towards the more landward part of North Bay and the lower South Bay with heavy influence of river outflow on its distribution in SFB. For the nutrient budget, the nutrient flux into coastal ocean through Golden Gate is largely balanced by the nutrient flux from North Bay. To study how suspended particulate matter can affect the light condition and phytoplankton growth of the ecosystem, a sediment transport model (SED3D) was further integrated with the coupled model. With SED3D, chlorophyll simulation was much improved. The analysis shows that euphotic zone depth (Ze) in SFB is limited by water depth in shallow regions (<2m), while Ze in deep regions is controlled by SPM concentration in the surface water. In addition, Ze is closely related to the primary production that varies from below 40 g[C].m^-2.yr^-1 to 160 g[C].m^-2.yr^-1 in northern SFB.