Lake Nanhu, a typical shallow urban lake in the middle and lower reaches of the Yangtze River, has undergone ecological evolution characterized by typical urban eutrophication due to long?term intensive anthropogenic activities. To reveal its long?term ecological response under continuous restoration efforts, this study integrated historical literature data from 1991-2022 with systematic field monitoring conducted from February 2023 to January 2025, analyzing the evolving trends, current status, and influencing factors of water quality and phytoplankton. Long?term data indicate that nitrogen and phosphorus concentrations followed three distinct phases: (1) a fluctuating rise beginning in the 1990s; (2) persistently high levels from 2003 to 2020, nitrogen and phosphorus concentrations persistently exceeded the Grade?V standard of China’s “Environmental Quality Standards for Surface Water” (GB 3838?2002); and (3) a downward trend after 2020, reflecting the initial effectiveness of implemented governance measures. Accordingly, phytoplankton abundance reached a peak of 1191.94 × 10? cells/L in summer 2017-2018 but declined markedly during 2023-2025. Nevertheless, the annual mean chlorophyll?a concentration remained high (61.08 μg/?L), indicating a continued risk of algal blooms. Recent monitoring showed that phytoplankton in Lake Nanhu were dominated by Cyanobacteria such as Pseudoanabaena and Microcystis in summer and autumn, with potentially toxigenic algae contributing up to 81% of total abundance, while Bacillariophyta, mainly represented by Cyclotella, prevailed in winter and spring. Both Pearson correlation and redundancy analysis (RDA) identified total phosphorus and water temperature as key environmental factors driving phytoplankton biomass and the dynamics of potentially toxigenic cyanobacteria. The results demonstrate that although long?term management has sub-stantially reduced nitrogen and phosphorus concentrations, phosphorus loading and its synergistic effect with water tem-perature remain critical in regulating algal biomass and sustaining the competitive advantage of toxigenic cyanobacteria. Therefore, future strategies must continue to strengthen the control of external phosphorus inputs and the suppression of internal phosphorus release.