The interannual variabilities of chlorophyll and nutrients in San Francisco Bay: a modeling study

San Francisco Bay (SFB) is a complex ecosystem that has been heavily impacted by human activities. It has experienced strong year-to-year variations in physical, chemical, and biological conditions, due to both natural climate variation and human activities. There is a need to investigate this long-term variation, with a focus on management practices and needs. The study aims to construct a coupled hydrodynamic and ecosystem model SCHISM/CoSiNE, to investigate interannual variability of chlorophyll and nutrient dynamics in SFB over the 10-year period of 2005–2014. The coupled SCHISM/CoSiNE model captures the long-term observations well. It shows that high chlorophyll concentrations in South Bay persist during warm months, while chlorophyll in North Bay is low and has strong interannual variation. Nutrient concentrations are higher in North Bay where large river outflow influences their distribution and interannual variation, and in lower South Bay. The model results show that phytoplankton blooms in Suisun Bay tend to occur when flow rates are between 100 and 250 m 3 /s and ammonium concentration is in the range of 1–2 mmol/m 3 . Model sensitivity experiments show that benthic grazing can potentially reduce phytoplankton biomass, and its effect on chlorophyll concentration is modulated by river outflow. We demonstrate the potential of this open-source model for exploring water quality conditions and options for river flow management of SFB.