The variation of river flow within a natural range plays an important role in promoting the social-ecological sustainability of a river basin. In order to determine the extent of the natural range of variation, this study assesses hydrologic flow thresholds for the Lower Ganges River Basin. The flow threshold was calculated using twenty-two “Range of Variability (RVA)” parameters. The impact of Farakka Dam on the Lower Ganges River flow was calculated by comparing threshold parameters for the pre-Farakka period (from 1934 to 1974) and the post-Farakka period (1975–2005). The results demonstrate that due to water diversion by the Farakka Dam, various threshold parameters, including the monthly mean of the dry season (December–May) and yearly minimum flows, have been altered significantly. The ecological consequences of such hydrologic alterations include the destruction of the breeding and raising grounds for a number of Gangetic species, the increase of salinity in the southwest coastal region of Bangladesh and a reduction of fish and agricultural diversity. The major findings in this paper have a number of policy-level implications to aid water sharing mechanisms and agreements between the government of Bangladesh and India. The methodological approach presented in this study is applicable to other river basins.