Abstract: To investigate the spatiotemporal evolution of water quality in important lakes in Wuhan, identify critical driving factors, and trace pollution sources, this study employed principal component analysis (PCA), Spearman’s rank correlation coefficients, and the APCS-MLR model to analyze eight lakes. The findings reveal that from 2013 to 2023, water quality in these lakes was predominantly classified as Class IV (GB 3838–2002 standard), followed by Class III. The dominant controlling factors were permanganate index, total phosphorus, total nitrogen, and dissolved oxygen. Analysis of interannual variations reveals a marked year-on-year upward trend in concentrations of all dominant controlling factors prior to 2019, while levels post-2019 have generally plateaued with occasional declines observed across all parameters except total phosphorus. Regarding intra-annual fluctuations, water quality during flood seasons demonstrates significantly poorer conditions compared to non-flood periods. Spatially, while historical and current distributions shared minor variations, lakes south of the Yangtze River generally maintained marginally better water quality than those north of the river. Pollution source apportionment reveals that intrinsic lake pollution sources and urban/rural non-point sources constitute the predominant contributors, jointly accounting for an average of nearly 80% of the dominant controlling factors. Consequently, prioritized efforts should be directed toward strengthening pollution prevention and control measures targeting intrinsic lake sources and non-point sources during flood seasons.