To explore the water ecological health of lake and river systems in Suzhou City, the phytoplankton community structure of 20 lake sampling points and 82 river sampling points in Suzhou City was investigated. Parameters were selected to express the phytoplankton index of biotic integrity (P-IBI) in the lake, such as the number of dominant species of phytoplankton, the Simpson index of phytoplankton, the total density of phytoplankton cells, and the percentage of cyanobacteria biomass, which were then used to evaluate the water ecological health of river and lake systems in Suzhou City. The results show that during the flood season (in July) and non-flood season (in October) in 2022, 108 species from seven phyla and 97 species from eight phyla of phytoplankton were found in the main lakes, respectively. In 2023, 125 species from eight phyla and 112 species from eight phyla were identified during the flood season (September) and non-flood season (May), respectively, with the highest number of species in the Chlorophyta, followed by the Bacillariophyta. In the main rivers, 150 species from eight phyla and 130 species from eight phyla of phytoplankton were detected during the flood and non-flood seasons in 2022, respectively, and they increased to 157 species from eight phyla and 168 species from eight phyla in 2023, respectively, with Chlorophyta and Bacillariophyta being the dominant species. There are significant spatial differences in the abundance and biomass of phytoplankton functional groups at each sampling point, with higher total abundance and biomass of phytoplankton functional groups during the flood season compared to the non-flood season.