In temperate regions, the occurrence of winter circulation in lakes is deemed to be less frequent or cease in the quite near future due to a climate-change-driven increase in surface water temperature. However, it is unclear how the disappearance of winter circulation affects phytoplankton communities. While water-temperature increase itself changes phytoplankton communities, the occurrence of winter circulation may influence phytoplankton communities independently the effect of water-temperature increase via different processes. Here, we analyzed the effects of winter circulation occurrence and water temperature on phytoplankton communities using long-term (37 years) monitoring records on 22 dam lakes in Japan. Specifically, we used Structured Equation Models (SEMs) to examine the direct and indirect effects of winter circulation (assuming dilution and material supply), water temperature, and nutrient concentrations on surface Chlorophyll-a (Chl-a), functional and taxonomic diversities of phytoplankton. The SEMs revealed that winter circulation indirectly decreased functional and taxonomic diversity by increasing total phosphorus concentration at the surface. The decrease in water temperature decreased Chl-a, functional, and taxonomic diversity. Our results showed seasonal decrease in water temperature simplified the community composition and reduced biomass, while the occurrence of winter circulation on community composition was complex and inconsistent across pathways. We suggest that climate change may alter lake properties through the loss of multiple physical processes, and the processes should be considered in future ecosystem predictions.