In many areas of the world, human consumption and climate change threaten freshwater inflows to coastal ecosystems. In the San Antonio Bay System, USA (SABS), freshwater inflows are projected to decrease in the coming decades. Our 30-month sampling period of SABS captured a prolonged period of higher inflows and a prolonged period of lower inflow. Our observations offer insights as to how this system might respond to lower freshwater inflows in the future. Of most importance in our observations was a regional shift that occurred in maximum primary productivity from the middle and lower SABS towards the upper SABS. In addition, a warm-month succession of phytoplankton taxa in the upper SABS that occurred during the wet period did not occur during the dry period. We also observed spatiotemporal shifts in apparent nitrogen- and phosphorus-limitation, with both appearing to influence phytoplankton biomass and primary productivity. Changes to SABS phytoplankton such as these might deleteriously affect organisms of higher trophic levels with life stages that are regionally confined by other factors, such as depth, macrophyte presence, and existence of hard-bottomed substrate, which in this bay system includes both commercially important and endangered species.