Globally, suitable freshwater habitats are undergoing alterations and fish population declines, primarily attributed to the swift changes in climate and land use. Developing an effective conservation policy for freshwater fish necessitates careful consideration of the impacts of climatic and spatial factors. This study focuses on the analysis of 64 threatened freshwater fish in Bangladesh to anticipate their current and future climatically suitable habitats, utilizing the bioclim() species distribution model. Additionally, this study examines existing inland hydrographic networks and their corresponding harvest rates. The findings indicate that approximately 75% of the area of occupancy for the studied species is currently climatically suitable, but this is expected to decrease to 13% under future climate scenarios. Notably, 27 threatened species are at risk of lacking climatically suitable habitats in the future within their current area of occupancy. The three components of hydrographic networks—floodplains, rivers, and natural lakes—play varying roles in providing a climatically suitable habitat for the studied species. For instance, only 34% of threatened fish species are projected to find a suitable habitat over flood areas, 23% over rivers, and 16% over lakes. Existing protected areas presently offer limited protection (21% suitable area), expected to decline to 6% in the future, with no dedicated protected areas for freshwater fish. Floodplains are highlighted for providing habitat connectivity and facilitating brood fish dispersal. However, the unregulated and unmonitored annual harvest of freshwater fish from floodwater and rivers poses a potential silent cause for rapid population decline. Prioritizing the management of hydrographic components to maintain habitat connectivity, legal protection for threatened fish species, and establishing permanent protected areas for fish are crucial aspects in developing a conservation policy to mitigate the impact of future climate scenarios on threatened freshwater species.