Freshwater inflow effects on phytoplankton have long interested aquatic ecologists. More recently, timing and magnitude of inflow events have been a focus as they can be strong drivers of phytoplankton diversity and productivity. In the present research, we empirically and theoretically explored the effects of inflow events on phytoplankton of Galveston Bay, Texas, a bay system whose freshwater inflow arises primarily from 2 rivers, the San Jacinto and Trinity. We found that conditions in the upper regions of Galveston Bay adjacent to these rivers had opposing influences on phytoplankton. In the region near the San Jacinto River, inflows mostly stimulated biomass and productivity, while in the region near the Trinity River, inflows had the opposite effect. This suggested that the phytoplankton reproductive growth rate was at times nutrient limited near the San Jacinto River and that population growth responded rapidly to nutrient loadings. This also suggested that population growth was controlled at times by other processes near the Trinity River, thereby negating the effects of nutrient loadings. Decreased phytoplankton biomass occurred in this region due, in part, to hydraulic displacement. These co-occurring and opposing inflow effects extended into the mid- and lower bay regions, but the extension varied in time and location with no seasonal trend. Such observations underscore the challenges of predicting system responses to altered inflows. Phytoplankton composition was also affected by inflows, and some taxonomic trends were regionally specific. Attributes of phytoplankton relating to use of alternative sources of nutrition, differential growth rates and immigration of euryhaline species from rivers likely influenced the spatiotemporal distribution of taxa.