The Danjiangkou Reservoir serves as a critical water source for the middle route of the South-to-North Water Diversion Project and is designated as a national first-level drinking water protection zone. Since the project‘s impoundment in 2014, the overall water quality in the reservoir area has consistently met or exceeded Class II standards, underscoring its vital ecological and water resource functions. Water level fluctuation, as a key operational parameter, directly shapes the aquatic environment and indirectly influences the growth, distribution, and diversity of phytoplankton. To evaluate how water-level-induced habitat changes affect phytoplankton functional groups in the Danku District of Danjiangkou Reservoir, this study conducted sampling and analysis during high-water (October-December 2023) and low-water (April-June 2024) periods. We examined the structure and composition of phytoplankton functional groups and the environmental drivers affecting them. A total of 128 phytoplankton species from 75 genera and 7 phyla were identified across varying spatiotemporal conditions. Chlorophyta (37.33%), Bacillariophyta (36.00%), and Cyanophyta (14.67%) dominated the phytoplankton community. Significant differences in functional group composition were observed across time and space. In total, 26 functional groups were identified, including groups N and P (adapted to mixed water columns), Y and T (suited to stagnant waters), and generalist groups M and Lo. During the high-water period, functional group B dominated in the main reservoir, whereas groups MP, P, and Lo were dominant during the low-water period. In the tributaries, groups M, Lo, and S₁ prevailed in the high-water period, while groups TC and B dominated in the low-water period. Redundancy analysis revealed that pH, turbidity, nitrate nitrogen, and phosphate were the primary environmental factors influencing dominant functional groups. Q-index-based water quality assessment indicated that the main reservoir water quality was generally “good”, while tributary water quality ranged from “poor” to “good”. These findings suggest that although water quality remains stable in the main reservoir, tributaries experience notable nutrient pollution impacts on phytoplankton communities during high-water periods, highlighting the need for management attention to external inputs under high-water conditions.