The relative importance of bottom-up versus top-down effects in aquatic ecosystems remains a longstanding and ongoing controversy. To investigate these effects on phytoplankton communities in freshwater lakes, phytoplankton and zooplankton were sampled, and physical-chemical variables were measured during spring and summer in two important freshwater lakes in northern China: Nansi Lake and Dongping Lake. The redundancy analysis results showed that phytoplankton density and biomass were regulated by physicalchemical variables (bottom-up effects) and predation (top-down effects) together, and the former was more prominent in both lakes. However, the correlation analysis indicated that the top-down effects of zooplankton on phytoplankton were not significant in spring and summer in both lakes, while the bottom-up regulation of physical-chemical variables on phytoplankton had different patterns in the two lakes. In Nansi Lake, the bottom-up effects of physical-chemical variables on phytoplankton were weaker in summer than that in spring due to the abundant nutrients in summer. In Dongping Lake, the bottom-up effects of physical-chemical on phytoplankton were significant both in spring and summer, and the dominant bottom-up control factor shifted from total nitrogen in spring to total phosphorus in summer, with an increased ratio of nitrogen to phosphorus due to changes in limiting factors. In the two studied lakes, with fish culture, the bottom-up effects of phytoplankton on zooplankton were more important than the top-down effects of zooplankton on phytoplankton. These results demonstrate the interactions between phytoplankton and zooplankton and highlight the importance of phytoplankton regulation in freshwater lakes, which has implications for the effective management of freshwater lake ecosystems.