Productivity and community structure of phytoplankton and zooplankton are influenced by hydrologic disturbances in many ways. In a recent modeling study it was suggested that pulsed inflows might enhance zooplankton performance, curb accumulation of phytoplankton accumulated biomass, and promote phytoplankton species diversity. We tested these predictions by performing microcosm experiments on natural plankton assemblages from the Nueces Delta, TX, USA. On three occasions (March, June, and September 2001), experiments of semi-continuous and flow-through design were conducted using natural plankton assemblages. We investigated the effect of two different inflow and nutrient loading regimes on zooplankton biomass, and phytoplankton biomass and diversity, i.e., continuous and pulsed inflows of 3 day frequency. Despite differences in initial community structure on these three occasions, as well as the very different communities that arose between experimental designs, our findings showed that pulsed inflows altered plankton dynamics. In all cases, pulsed inflows resulted in greater zooplankton biomass. In most cases, pulsed inflows resulted in lower phytoplankton biomass and higher diversity. We speculate that greater phytoplankton diversity in the pulsed flow treatments favored selectively feeding zooplankton, whose better performance prevented higher accumulation of phytoplankton biomass.