Abstract: In order to explore the community structure and primary driving factors of phytoplankton in overlying water lakes, this study selected Shaobo Lake, a typical overlying water shallow lake, as the research site. Over three seasons, from 2021 to 2022, sampling surveys of the phytoplankton community in Shaobo Lake were carried out. A total of 138 species, belonging to 8 phyla and 59 genera, were identified. Among them, 51 species were presented in the wet season, 97 species in the dry season, and 86 species in the normal season. From the perspective of distribution in the lake, the annual average biomass and abundance of phytoplankton in Shaobo Lake ranged from 7.90 to 14.21 mg·L^-1 and from 1.27 × 10⁷ to 2.28 × 10⁷ L^-1, respectively. The biomass and abundance gradually decreased from the upstream to the downstream. There was a pronounced hydrological succession in the phytoplankton community structure. With the Microcystis aeruginosa, Chroococcus limneticus and Microcystis as the predominant succession, the dominant species display a hydrological variation. Diversity analysis shows that the mean values for the Shannon-Wiener Index, Pielou Index and Margalef Index in three seasons ranged from 0.41 to 2.01, 0.07 to 0.21, and 3.02 to 5.83, respectively. Generalized Additive Model (GAM) analysis indicates that temperature (WT), transparency (SD), and nitrate nitrogen (NO₃^--N) were the primary environmental factors affecting phytoplankton biomass, while chlorophyll-a (Chl-a) and dissolved oxygen (DO) were critical environmental factors influencing biodiversity.