In order to reveal the differentiated responses of plankton and zoobenthos to water quality on both annual and seasonal time scales, an ecological study on plankton and zoobenthos community was conducted during 2011 to 2015 in Nansi Lake in northern China. Different dynamics were found among phytoplankton, zooplankton, and zoobenthos in terms of density, biomass, and biodiversity. On an annual time scale and with deterioration of water quality, density and biomass of plankton and zoobenthos showed different variations, while phytoplankton (density, biomass, and biodiversity) changed significantly when water quality improved. On a seasonal time scale, density and biomass of phytoplankton showed significant differences between spring and summer. Results of Pearson’s correlation analysis revealed that phytoplankton, zooplankton, and zoobenthos were significantly affected by different environmental factors. Our study demonstrated that phytoplankton was more sensitive to water quality changes than zooplankton and zoobenthos. These results suggest that density and biomass of phytoplankton could rapidly reflect water quality, whereas biodiversity of phytoplankton could indicate long-term status of water quality combined with the physico-chemical parameters of water. The results could contribute to predicting the dynamics of plankton and zoobenthos in freshwater lakes and to selecting effective bio-indicators for ecosystem health assessment of freshwater lakes.