This study investigates how lake morphology, water quality, and water-level fluctuations (WLF) collectively shape wetland plant communities across 90 lakes in the Republic of Korea. By analyzing morphological indices (Index of Basin Permanence; IBP, Rawson Index; RI), WLF, water quality, and vegetation data, we identified four distinct lake groups through cluster analysis. Group C, comprising large dams, was characterized by the highest IBP and extreme WLF. Despite having favorable water quality, this group exhibited the lowest species richness, suggesting that severe physical disturbance from WLF is a primary limiting factor for wetland plant community. In contrast, Group A (estuarine reservoirs) showed stable water levels but high nutrient concentrations, which led to eutrophic conditions and communities dominated by a few tolerant species. Group D, which included small agricultural reservoirs and floodplain wetlands, had complex shorelines (highest RI) and supported the higher diversity of aquatic plants. This indicates that habitat heterogeneity can mitigate moderate physical disturbances and enhance richness. Canonical Correspondence Analysis and Variation Partitioning Analysis revealed that community structure is primarily influenced by hydrological disturbance, chemical stress (eutrophication), salinity, and shoreline complexity. These analyses confirmed that the interplay of these environmental factors explains community variation more effectively than any single factor alone. Our findings demonstrate that lake plant communities are shaped by a complex interaction of geomorphological, hydrological, and chemical factors. Therefore, effective lake management must adopt an integrated approach, considering both water-level regulation and shoreline complexity to enhance ecological integrity.