Seasonal phytoplankton dynamics in lakes are highly sensitive physicochemical changes in the water column. As climate-driven frequency and variability of precipitation increases, lakes may experience increased inputs of allochthonous organic matter and nutrients through pulsed rain events. The resultant effects of lake physicochemistry on phytoplankton seasonal succession and assemblage are poorly understood. In the current study, the phytoplankton assemblage of a subtropical monomictic lake was examined in the context of natural interannual oscillations in allochthonous dissolved organic carbon and nutrient inputs resulting in prolonged clear-water and dark-water phases over a 14-year period. Differences in water clarity and nutrient concentrations among phases caused pronounced assemblage and morphology-based functional grouping shifts largely associated with hydrologic effects of the Pacific Decadal Oscillation. Determining how phytoplankton assemblages respond to changes in allochthonous supplies is critical to understanding and predicting the cascading effects of climate on lake ecosystems at all latitudes