Bangladesh is rich in freshwater biodiversity, but information on riverine fish diversity is lacking. This study represents a complete list of fish species of Dhepa, Punarbhaba, and Atrai rivers of Bangladesh based on surveys carried out for seven years, from 2009 to 2016. A total of 121 species belonging to 80 genera and 33 families were recorded, of which Cyprinidae was the most dominant family representing 24 species. A total of 42 threatened species and 10 exotic species were collected during the survey. This study highlights that Dhepa, Punarbhaba, and Atrai are critical habitats for many conservation-concern fish species, and reveals the need for developing suitable conservation and management plans for the future.