Lakes within river-floodplain ecosystems are key biodiversity refuges majorly threatened by eutrophication and hydrologic river-lake fragmentation. However, an integrative index, specifically designed to comprehensively assess the health of floodplain lakes, considering multiple biological taxa and major stressors, remains unavailable. Based on biological data collected from 68 isolated lakes in the eastern plain lake region of China, we constructed a reliable index for assessing floodplain lake ecosystem health: Integrated Bioassessment Index (L-IBAI). The L-IBAI consists of components of overall health and species diversity, eutrophication, and hydrological connectivity and water level regimes. To construct the L-IBAI, we firstly used the observed species (SO)-area (A) model to predict the expected species richness (SE), and then developed observed to expected indices by calculating the SO/SE ratio for fish (F-O/E-SA) and benthos (B-O/E-SA). The health level thresholds for the other four indices, namely the ratio of Secchi depth and water depth (ZSD/ZM), chlorophyll a in phytoplankton (Chl a), the percent of rheophile fish species, and emergent macrophytes coverage, were determined using cumulative frequency curves. The final L-IBAI score was obtained by summing the weighted values of the three components mentioned earlier. The L-IBAI can significantly discriminate rural from urban lakes, and is a reliable index for assessing lake ecosystem health. Moreover, we developed three simplified three-index integrated bioassessment indices, which consists of three indices belonging to the three elements are also effective. The developed L-IBAI is flexible to be extended and applied to other floodplain lakes, and outcomes of health assessments for the eastern plain lakes in China helped to identify conservation and restoration priorities.