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1. The effect of variability in rainfall on the potential for algal blooms was examined for the St Johns River in northeast Florida. Water chemistry and phytoplankton data were collected at selected sites monthly from 1993 through 2003. Information on rainfall and estimates of water turnover rates were used in the analyses of trends in phytoplankton biomass. 2. Major trends in rainfall and runoff within the lower St Johns River catchment over the 10-year study period were marked by both significant drought and flood periods. Autumn and winter rainfall patterns were strongly correlated with the range of Pacific sea surface temperature anomalies associated with El Niño events and La Niña periods. The effect of these major shifts in rainfall was evident in the strong relationship to replacement rates for water within the lower St Johns River. 3. The eutrophic status of the river was reflected in the high concentrations of nitrogen and phosphorus observed at all sampling sites, with total nitrogen concentrations up to 3100 μg L−1 and total phosphorus concentrations up to 180 μg L−1. 4. While it is clear that the high phytoplankton biomass and frequent blooms that characterize the freshwater portions of the lower St Johns River are fundamentally based on nutrient status, the expression of that potential was strongly correlated to water replacement rates, as revealed by the inverse relationship between phytoplankton biovolume increase and water turnover rate, with an R2 of 0.80 for the major bloom season. The sensitivity of algal blooms to rainfall patterns over the 10-year study period suggest that longer-term temporal and spatial shifts in rainfall, such as multi-decadal cycles and the global-warming phenomenon, will also influence the frequency and intensity of algal blooms. [ABSTRACT FROM AUTHOR]