Understanding biodiversity and community composition is a prerequisite to sustainable exploitation and conservation of fisheries. We assessed the spatial and seasonal patterns of fish community composition and biodiversity in seasonal no‐take riverine sanctuaries in Bangladesh, which aim to conserve the anadromous hilsa shad (Tenualosa spp. and Hilsa keele). Fish samples were collected during monsoon, as well as pre‐ and postmonsoon, from five sites within two sanctuaries and one site in an open fishing area. Although total abundance was similar along the rivers, species richness was significantly higher at the open fishing site due to its connectivity to nearby habitats. The diversity apparently decreased in a downstream direction. Fish communities at two upstream sites were separated from other sites in multivariate space largely due to higher abundance of hilsa at downstream sites and presence of floodplain‐oriented species at the two upstream sites. Short body length and high trophic level at all sites indicated that fish communities were overexploited. Our results also indicated that riverine hilsa sanctuaries in Bangladesh are rich in fish species diversity and support several threatened species designated by the International Union for Conservation of Nature (IUCN). Our study also suggested that since hilsa abundance shapes community patterns, it can therefore impact riverine ecosystem functioning in the sanctuary areas. The findings of this study can serve as an important baseline for future biodiversity assessment, conservation and impact assessment of conservation in rivers, and therefore help to establish multispecies ecosystem‐based management of riverine fisheries around the world.