This report analyzes trends in long-term water quality indicator data in San Francisco Bay, with a focus on chlorophyll-a concentrations, gross primary production, and dissolved oxygen concentrations (DO). Chlorophyll-a concentrations correlate with the total amount of phytoplankton present, while gross primary production encompasses the total amount of photosynthesis occurring. The data come from bi-weekly to monthly cruises that collect samples at fixed stations along the Bay’s deep channel. This analysis looked at data collected between the Central Bay, near Alcatraz, and the Lower South Bay, just south of the Dumbarton Bridge. Data were assessed annually and seasonally, with a focus on August through October (AugOct) to align with seasonal windows used in previous studies. 

The analysis found that phytoplankton production began increasing across the Central, South, and Lower South Bays beginning in the 1990s. Notably, annual gross primary productivity in the early 1990s increased to rates that were two to three times higher by the mid to late 2000s. Productivity in the Central Bay and the northern South Bay then plateaued between 2010 and 2019. However, the trend reversed over the same time period at the southernmost stations, where productivity decreased to rates that were comparable to the early 1990s. This suggests that different mechanisms impacted phytoplankton productivity in the different subregions of the Bay. Despite strong seasonal and interannual variability, DO concentrations from the Central Bay to the South Bay rarely dropped below the Water Board’s San Francisco Bay Basin Plan standard of 5 mg/L, while one station in the Lower South Bay had occasional observations that dropped below. When looking at 10-year windows of DO data, Seasonal DO_AugOct did not show any statistically significant changes. However, when trends were evaluated over longer windows, three stations showed significant decreases, suggesting different analyses may provide valuable insights from the DO data. Preliminary analyses of suspended sediment, turbidity, and dissolved inorganic nitrogen raise questions for continuing work, which will also include extending trend analysis to San Pablo and Suisun Bays.