We examined how freshwater flow and phytoplankton biomass affected abundance and population dynamics of the introduced subtropical copepod Pseudodiaptomus forbesi in brackish and freshwater regions of the San Francisco Estuary, California, USA. This copepod is key prey for the endangered and food-limited delta smelt, Hypomesus transpacificus, in low-salinity water during summerautumn. Long-term monitoring data showed that P. forbesi was most abundant in fresh water, where summer-autumn abundance was invariant with freshwater flow. Abundance was positively related to freshwater flow in low-salinity water. Reproductive rates in both regions during 2010-2012 were low and unresponsive to chlorophyll or freshwater flow. Development indices, calculated as ratios of laboratory-derived to field-derived stage durations, were lowest for nauplii and highest for late copepodites, but averaged below 0.5 for all stages combined. Development indices were weakly related to chlorophyll for late copepodites only, unrelated to freshwater flow, and slightly higher in low-salinity than fresh water. Thus, the principal mechanism by which flow affects the P. forbesi population is apparently transport of copepods from fresh water to low-salinity water, where copepods are available to delta smelt. This work demonstrates how freshwater flow affects estuarine foodwebs through spatial subsidies of food supply.