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The rising challenge of eutrophication in aquatic systems globally necessitates an understanding of phytoplankton community dynamics under diverse biomanipulation approaches. This study, conducted from June 2022 to July 2023 in the Yuqiao Reservoir’s ponds in China, explored phytoplankton dynamics across ponds under different biomanipulation strategies. The study included a pond (BL) without fish stocking, a pond (CH) stocked with carnivorous and herbivorous fish, and another pond (CFD) incorporating a mix of carnivorous, filter-feeding, and detritus-feeding fish. Substantial seasonal variations in phytoplankton density and biomass were observed. In the BL pond, phytoplankton density ranged from 0.23 × 10⁷ to 3.21 × 10⁷ ind/L and biomass from 0.71 to 7.10 mg/L, with cyanobacteria predominantly in warmer seasons and a shift to cryptophytes and chrysophytes in winter. The CH pond exhibited a density range from 0.61 × 10⁷ to 8.04 × 10⁷ ind/L and biomass of 1.11 to 7.58 mg/L. Remarkably, the CFD pond demonstrated a significant reduction in both density (0.11 × 10⁷ to 2.36 × 10⁷ ind/L) and biomass (0.27 to 5.95 mg/L), indicating the effective implementation of its biomanipulation strategy. Key environmental factors including total nitrogen, water temperature, pH, chlorophyll-a, and total phosphorus played a significant role in shaping phytoplankton communities. The study highlights the importance of tailored biomanipulation strategies in aquatic ecosystem management, emphasizing long-term monitoring for sustainable management of eutrophication.