Abstract Climate change is expected to drive significant alterations in rainfall patterns, which will pose considerable threats and pressures on aquatic ecosystems. Phytoplankton, as a critical component of these ecosystems and a reliable biological indicator of environmental health, may respond variably to such climatic changes. However, our understanding of how phytoplankton communities respond to climate change remains limited. In this study, we investigated the response of phytoplankton functional groups to rainfall patterns and their relationships with environment factors in a subtropical eutrophic lake (Changhu Lake, China) from May 2020 to April 2022. Our findings indicate that changes in phytoplankton functional structure over time were influenced by rainfall patterns. A total of 119 genera, 21 functional groups, and 15 dominant functional groups were identified, with the dominant functional groups exhibiting strong seasonal variations. Notably, shifts in rainfall patterns led to a transition in dominant phytoplankton functional groups: from taxa tolerant of mixing and low nitrogen levels (e.g., H1, J, and S1) during the rainy season to taxa that thrive under eutrophic and stratified conditions (e.g., X2, C, N, and W1) during the dry season. The use of phytoplankton functional approaches simplifies identification and reflects environmental conditions effectively. Redundancy analysis (RDA) revealed strong correlations between changes in phytoplankton functional groups and environmental factors such as water temperature, precipitation, water level, and nutrient availability. The insights from this study improve our understanding of how aquatic ecosystems shift under climate change and demonstrate the potential of phytoplankton functional responses as a valuable tool for water management and conservation.