The remnant populations of Gharials, Gavialis gangeticus, are now confined to the large, deep rivers of northern India and Nepal. In lowland Nepal, the populations are restricted to a few stretches of the Narayani–Rapti and Karnali–Babai river systems. Periodic censuses of the wild populations have been made over the past 12 yr. Here, we present population trends of Gharials in the Narayani, Rapti, and Babai rivers based on these surveys. The results indicate that the combined numbers of adults and subadults have been gradually increasing since 2005, but the numbers of adults are low and female biased, with very few males recorded from all study sites. In 1978, Nepal established a captive breeding center in Chitwan National Park, from which captive-bred animals have been periodically released 4–7 yr after hatching, at which time the animals are about 1.5 m total length. The detection of hatchlings and subadult classes that are smaller than these released animals in the rivers indicates that there is natural recruitment. Therefore, collecting all nests for ex-situ breeding might not be the best strategy until more rigorous field assessments are completed to determine the relative contributions of captive-bred versus natural recruitment. We suggest that more effort should be channeled toward field assessments, including mapping and monitoring habitat availability, habitat management to ensure necessary environmental flows to create sand banks and deep pools, and research to better understand the ecology and behavior of Gharials in Nepal's rivers.