<p>Lakes provide vital ecosystem services, yet intensified human activities have caused ecological degradation in lake-based urban agglomerations, leaving the mechanisms behind human–ecosystem conflicts unclear. Using the Chaohu Lake urban agglomeration as a case study, this research integrates remote sensing data, fuzzy membership functions, the random forest model, and spatial analysis methods to investigate the spatiotemporal patterns and formation mechanisms of human–ecosystem service conflicts, addressing research gaps in understanding complex human–ecosystem interactions in lake-based urban agglomerations, especially nonlinear relationships. The results indicate a decline in total conflicts after 2010, with high-conflict zones persisting in ecologically sensitive and urban fringe areas, notably on the northeastern shore of Chaohu Lake, around the Lujiang urban core, and in central Fanchang. There are significant nonlinear constraint relationships between human activities and ecosystem services, including inverted U-shaped, U-shaped, and convex decline patterns, consistent with ecological economic interpretations of threshold effects. Conflict formation evolved from industrialization-driven to urbanization-dominated and later to governance-regulated phases, reflecting the progressive shift from economic expansion toward ecological restoration. The proposed governance framework integrating institutional, planning, and engineering dimensions emphasizes the importance of coordinated management, spatial optimization, and system restoration. This study contributes to a deeper understanding of interactions between human activities and ecosystems in lake-based urban regions, and provides policy-relevant insights for achieving a balance between ecological security and sustainable development in the Anthropocene.</p>