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Climate change affects seasonal weather patterns, but little is known about the consequent effects on phytoplankton assemblage variation. We studied the changes in phytoplankton assemblages, expressed as morpho-functional groups, during four seasons over the past two decades in large shallow eutrophic Lake Taihu, China. During this period, both climate and nutrient levels changed in the lake. Wind speed declined significantly from 1997 to 2016 in all seasons, while global radiation increased significantly in spring and winter. Phosphorus and chlorophyll a concentrations showed a significant increasing trend in all seasons, especially in summer and autumn. Diatoms, mainly Aulacoseira and Asterionella, increased during late winter and early spring. Multiple stepwise regression analysis and non-metric multidimensional scaling indicated that climatic variables (i.e., decreasing wind speed and increasing global radiation) were the main drivers of phytoplankton assemblage variance in winter and early spring. An increase in the dominance of cyanobacteria (mainly Microcystis spp.) in summer and autumn was mainly related to changes in phosphorus. Our results indicate that both nutrients and climatic variables were major drivers of the observed changes in phytoplankton assemblages, differing in importance between seasons. The differential response of phytoplankton community variation to future environmental change in the different seasons needs to be taken into account when evaluating the long-term changes in phytoplankton.