We quantitatively analyzed the changing patterns of phytoplankton after being treated by purification units in this study with three groups of recirculating pond aquaculture systems—a composite pond recirculating aquaculture system (A), a paddy field-fish pond recirculating aquaculture system (B), and a combined wetland-pond recirculating aquaculture system (C)—to explore the influence law of aquaculture water purification on phytoplankton community structure and diversity. The removal efficiency of different pollutants varied among the three systems, with system A having the highest removal efficiency for potassium permanganate index, total nitrogen, and suspended solids, whereas system C had the lowest efficiency for these contaminants. Compared to the inflow water, the Chl a concentrations in the effluent water were decreased by 52.08%, 67.61%, and 27.06% in systems A, B, and C, respectively. During the study period, 138 species from seven phyla of phytoplankton were identified, which were dominated by species from Chlorophyta, Cyanophyta, and Bacillariophyta. The number of phytoplankton species varied between the different systems; however, the dominant species and their dominance were not significantly different. Compared to the inflow water, the density and biomass of different phytoplankton species in the purification units were substantially decreased in systems A and B, and the algal removal rates exhibited an increasing trend along the cross-sections of the purification unit. Phytoplankton density fluctuated greatly in the purification unit of system C. Overall, phytoplankton species from different phyla were similarly affected by the purification units. The diversity of phytoplankton in the purification units was increased compared to the inflow water in the three systems, with the H′ and J index values increasing significantly in systems A and B (P＜0.05). Pearson correlation and redundancy analyses indicated that the densities of phytoplankton were significantly positively correlated with factors such as total phosphorus, total nitrogen, and potassium permanganate index in the water (P＜0.05), but there were differences in the factors influencing phytoplankton among different systems. This study revealed that aquacultural water purification significantly affects the phytoplankton community. Optimizing the purification unit environment may be useful for improving the purification efficiency of pollutants and phytoplankton.