River flow regulation by dams and barrages threatens freshwater fish diversity globally. However, factors contributing to the recovery of fish communities downstream of barriers to river flow are not well understood. It is crucial to identify processes that might enable river restoration despite the presence of river barriers. In this study, we assess recovery of fish species, including endemics, downstream of large and small barriers in the Malaprabha basin in the Western Ghats of India. We define “fish species recovery” as the proportion of fish species occurring in river reaches downstream of barriers, of the species pool occurring in upstream unregulated segments with similar elevation, stream order, and habitat characteristics. As per the serial discontinuity concept, we predicted that recovery will reduce immediately after, but gradually increase with, increasing distance downstream of barriers, due to contributions from unregulated streams joining the river. As expected, fish recovery decreased immediately downstream of barriers and increased at greater distances and declined when the number of upstream barriers increased, indicating cumulative impacts. Dissolved oxygen and total alkalinity were positively and negatively correlated with both recovery and distance from barrier. Water temperature and rocky instream habitat influenced recovery positively, but independent of distance from barriers. Recovery of fish species, including Western Ghats endemics, was promising even under the current level of river regulation in the area, mainly due to connectivity with undammed tributaries. Strict limits on future stream regulation within already regulated basins will be critical for conservation of freshwater fish biodiversity in this region.