In peninsular Florida, USA, rainfall is coupled with the Pacific Sea Surface Temperature Anomaly (SSTA), and rainfall affects mean depth and residence time of shallow lakes. We examined effects of two cycles of variation in rainfall using a 15-year data set from a shallow eutrophic lake dominated by small zooplankton, cyanobacteria and omnivorous fish. In high rainfall periods, the lake was deeper and cladoceran biomass was significantly higher than in dry periods. One factor was correlated with reduced biomass of cladocerans: a 3-fold higher biovolume of cyanobacteria. This led us to examine how variation in rainfall affects cyanobacteria. When cyanobacteria biovolume was high, the movement of water through the lake was low and invariant. Cyanobacteria grew unchecked. When cyanobacteria was reduced and cladocerans attained high biomass, there were intermittent flushing events that may have disrupted algal growth. Water color was elevated ∼6-fold during the same time periods. Greater color may have made conditions less favorable for cyanobacteria by increasing light attenuation, and also more favorable for cladocerans, by reducing risk from fish. This study provides insight into how future variability in rainfall and drought, which may be exacerbated by global warming, could affect plankton in shallow subtropical lakes.