Hydrodynamic Modeling Coupled with Long-term Field Data Provide Evidence for Suppression of Phytoplankton by Invasive Clams and Freshwater Exports in the San Francisco Estuary

The San Francisco Estuary (California, USA) had abundant pelagic fish in the late 1960s, but has few pelagic fish today. A primary cause for this decline in fish is thought to be a trophic cascade, triggered by declining phytoplankton. Here, we describe the changes in pelagic community structure of the San Francisco Estuary. Then, we examine whether changes in hydrodynamics due to freshwater exports, which increased exponentially beginning in 1967, in addition to the 1986 invasion by the clam Potamocorbula amurensis, explain the phytoplankton loss. Hydrodynamic variables were reconstructed back to 1956 using statistical models fit to, and cross-validated against, output from a hydrodynamic model. Then, we regressed mean summer/fall chlorophyll a—the season with the largest phytoplankton decline—against the reconstructed hydrodynamic variables and the presence/absence of P. amurensis for 1969–2014. The regression model, which explained 78% of the interannual variation in chlorophyll a, was then used to quantify the influence of P. amurensis and exports on chlorophyll a. Based on monitoring data, chlorophyll a declined 22-fold from 1969–2014, zooplankton declined 32-fold from 1972–2014, and pelagic fish declined 92-fold from 1968–2014. Averaged over 1990–2014, the chlorophyll a model ascribed an 88% decline in chlorophyll a to P. amurensis, a 74% decline to exports (at minimum), and a 97% decline to the combined influence of P. amurensis and exports (at minimum). Thus, the decline in pelagic productivity in the San Francisco Estuary has occurred largely due to the combined impacts of the P. amurensis invasion and increased freshwater exports.