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In 1992, damming was performed in Punarbhaba river (India and Bangladesh), disturbing water flow and riparian wetland ecology. We measured the eco-hydrological failure rate, degree of flooding alteration and degree of eco-hydro deficit in relation to indicators of hydrological alteration in riparian wetlands. Normalized Differences Water Index (NDWI) and Modified Normalized Differences Water Index (MNDWI) images derived from Landsat satellite images were studied. A greater intensity of NDWI and MNDWI score were associated with the higher amount of water availability and therefore, monthly NDWI and MNDWI values were used. We showed that due to the attenuation of water availability (52% in pre-monsoon season, 34% in monsoon, and 32% in post-monsoon seasons), most months had a considerable decrease of NDWI/MNDWI scores, often below acceptable ecological thresholds. The registered failure rates for attaining the eco-hydrological threshold exceeded 100%. The estimated degree of flooding alteration in the larger parts of wetlands reached 100%, indicating a high degree of impact. Up to 54% of wetlands were eco-hydrologically deficit and 36% of wetlands were critically affected. Sustenance of ecological flow is necessary to reduce the growing hydrological crisis of the wetland habitat and ecosystem.