Lentic ecosystems, including lakes, reservoirs, and marshes, are vital ecological assets increasingly threatened by anthropogenic pressures, necessitating robust tools for assessing their biological integrity. This study aimed to develop and apply an aquatic plant-based Multi-metric Index (MMI) to evaluate the biological integrity of 90 lentic systems (primarily lakes and reservoirs) across the Republic of Korea, using a standardized dataset from a three-year national monitoring program (2022~2024). We selected eight metrics based on their ecological relevance, sensitivity to disturbance, and scientific robustness. These were organized into three categories: Species richness (30% weight), eutrophication and disturbance (30%), and habitat integrity (40%). Scoring criteria for each metric were established using cumulative distribution functions, and the final MMI scores were used to classify the ecosystems into five integrity classes (A: Excellent to E: Very Poor). The assessment revealed that the majority of the surveyed ecosystems (87.8%) were in a moderate to slightly poor state (Classes B, C, and D), with only 4.4% classified as excellent. Widespread loss of submerged and floating leaved aquatic plants suggests that many domestic lentic systems may be approaching or have already undergone a regime shift to a turbid, phytoplankton-dominated state. This MMI provides a scientifically-defensible tool for managing lentic ecosystems, underscoring the urgent need to restore aquatic plants communities by improving underwater light conditions and rehabilitating littoral habitats.