Floodplain wetlands in their optimum habitat condition act as the preventive mechanism from environmental degradation like pollution, lowering of groundwater table, flood, temperature control and others. Therefore, the protection and stability condition assessment of these wetlands are very much indispensable for the sake of the environment. In the present work, the habitat stability assessment of the wetlands of a floodplain region produced by River Ganga has been done considering the hydro-geomorphological (HGM) and surface water availability (SWA) parameters. The fuzzy classification (FC) and composite indexing (CI) method have been applied to perform the analysis. The result suggests that 16%–24% of wetland area is very highly prone to loss and 33%–36% area needs proper management whereas only 9%–11% wetlands are very highly stable. The wetlands have shown a rise in the average seasonal water level fluctuation from 2.18 m in 2014 to 3.38 m in 2018 which indicates more drying out condition during lean months. From morphogenetic perspective, nearly 43% of wetlands are riverine and in terms of HGM classification 77% of the wetlands are groundwater depressions (GWD). So, lack of water supply all throughout the year, seasonal water level fluctuation and absence of active river-wetland links are mainly responsible for the degradation of habitat stability condition of the wetlands. The results have been validated over different ground locations using kappa index and ROC curve method. It suggests that both these methods are very much accurate and between these two, FC method has given better result.