In aquatic ecosystems, the dynamics of ecological parameters play an important role in community organizations. To understand the seasonal variation in the phytoplankton community in Lake Wuchang, Anhui Province, water samples were collected in three different hydrological periods (dry season, normal season, and wet season) from December 2019 to August 2020. The dominance value (Y), niche width (Bi), niche overlap (Oij), variance ratio method (VR), chi-squared test (χ2), and association coefficients were used to analyze the niche and interspecific association with respect to the dominant phytoplankton species in different hydrological periods, while the redundancy analysis method (RDA) was used to distinguish the key driving environmental factors for the dominant phytoplankton species. The results showed that 308 species belonging to 8 phyla were identified, of which 13 species from 4 phyla were the dominant species. From the dry season to wet season, the dominant species changed from Bacillariophyta to Cyanophyta, while Synedra acus was the dominant species throughout the hydrological periods. The niche width of the dominant species varied from 1.77 to 6.65, and the niche width of Dinobryon was the lowest, while that of Synedra acus was the highest. The niche overlap showed temporal and spatial differences, of which 30 dominant species pairs were greater than 0.600, indicating that they occupied the environmental resources in a highly similar way. The interspecific association results showed that there was a significant positive correlation between the dominant species, especially in normal and wet seasons. Only 10 of the 48 dominant species pairs had significant associations based on the χ2 test, and two pairs had negative associations in the wet season, which might be related to the hydrological condition in the wet season. According to redundancy analysis, NO3−-N, NH4+-N, PO43--P, water depth (WD), and water temperature (WT) were the key environmental factors affecting the phytoplankton community variation in Lake Wuchang. This paper provides a new perspective for the study of the early warnings regarding the cyanobacteria bloom outbreak, and the management and protection of the water ecological environment in shallow lakes in the middle and lower reaches of the Yangtze River.