Rebuilding a clear-water state dominated by submerged macrophytes is essential for addressing eutrophication, yet the impact of benthic fish on water quality is complex. We conducted two experiments to explore the interaction of submerged plants and benthic fish on the water quality. Experiment I investigated the water clearing effects of submerged macrophytes with varying coverage (from 0% to 40%) before and after the removal of benthic fish. Experiment II explored the impacts of benthic fish at different densities on aquatic ecosystems with and without submerged macrophytes. The results showed that an increase in submerged macrophytes coverage significantly enhanced the reduction of some major water quality parameters. We assert that the coverage of submerged macrophytes should not be lower than 40% to establish and sustain a clear-water state in shallow lakes. However, benthic fish significantly weaken the ability of submerged macrophytes to improve water quality. Surprisingly, the presence or absence of macrophytes may reverse the role of benthic fish in freshwater ecosystems. When macrophytes are present, benthic fish can cause water quality to deteriorate. Conversely, when macrophytes are absent, benthic fish with a density of ≤ 10 g/m