Reservoir bays are sensitive areas in terms of water quality and safety. This study analyzed water quality in the Danjiangkou Reservoir in China. Specifically, seasonal patterns and drivers of phytoplankton in the reservoir were explored during dynamic water diversion processes. Water quality and phytoplankton community samples were collected from 18 representative sites ranging from the inlet to the outlet of the reservoir, and samples were collected seasonally from July 2018 to July 2019. In the entire reservoir, the total abundance of phytoplankton ranged from 0.43×10³ to 4.7×10⁶ cells/L, with the highest abundance in summer and lowest in autumn. The Shannon-Wiener diversity index was the highest in spring and lowest in autumn. The phytoplankton community was composed of diatoms-Chlorophyta in spring, Chlorophyta-diatoms in summer, cyanobacteria in autumn, and cyanobacteria-Chlorophyta-diatoms in winter. The relative abundance of cyanobacteria was highest in autumn. Conductivity, total nitrogen (TN), total phosphorus (TP), and chlorophyll-a were all highest in autumn, and cyanobacteria abundances were the highest in Huzhai Bay. An obvious succession of phytoplankton communities was observed from the inlet to the bay to the outlet. For hydrological factors, reservoir water levels were the highest in autumn, during which the regulating flow velocity and flow capacity increased. Linear regression analysis showed that water levels were negatively correlated with diversity indices. Variation partitioning showed that stochastic factors and physicochemical factors both influenced the formation of phytoplankton communities. The partial Mantel test indicated that the phytoplankton community composition in bays was correlated with the water temperature, oxidation-reduction potential, chemical oxygen demand, TN, and TP. Canonical correspondence analysis showed that TN was the most significant factor affecting the composition of phytoplankton communities in bays. These findings should be useful for future efforts to improve water quality in the Danjiangkou Reservoir.