This paper studied the community structure and diversity of phytoplankton and macrobenthos in four larger lakes in Jiangsu Province from December 2018 to August 2019. The results showed that the density, biomass, the dominant species and diversity were significantly spatial and temporal differences（P<0.05）. The density and biomass of phytoplankton and benthic animals were the highest during the high flow period, and the Margalef richness index and the ShannonWiener diversity index exhibited a consistent trend. The phytoplankton population was dominated by Chlorophyta. The algae density of Gaoyou and Baima Lakes reached the level of mild bloom, and the dominant species of phytoplankton in each lake were the algae that easily cause blooms. The phytoplankton species diversity evaluation grades of all lakes were medium to relatively rich. The benthic animals were mainly composed of Chironomidae larvae, Bivalvia and Malacostraca, while the dominant species were Chiroptera larvae and Oligochaete, the species diversity assessment grade was poor to medium. Phytoplankton algae density increased in lakes, but macrobenthos sensitive species decreased,indicating that the environmental pressure on lakes increased, the structure of aquatic communities changed, and diversity decreased.