The gharial (Gavialis gangeticus Gmelin) is a fish-eating specialist crocodylian, endemic to south Asia, and critically endangered in its few remaining wild localities. A secondary gharial population resides in riverine-reservoir habitat adjacent to the Nepal border, within the Katerniaghat Wildlife Sanctuary (KWS), and nests along a 10 km riverbank of the Girwa River. A natural channel shift in the mainstream Karnali River (upstream in Nepal) has reduced seasonal flow in the Girwa stretch where gharials nest, coincident with a gradual loss of nest sites, which in turn was related to an overall shift to woody vegetation at these sites. To understand how these changes in riparian vegetation on riverbanks were related to gharial nesting, we sampled vegetation at these sites from 2017 to 2019, and derived an Enhanced Vegetation Index (EVI) from LANDSAT 8 satellite data to quantify riverside vegetation from 1988 through 2019. We found that sampled sites transitioned to woody cover, the number of nesting sites declined, and the number of nests were reduced by > 40%. At these sites, after the channel shift, woody vegetation replaced open sites that predominated prior to the channel shift. Our findings indicate that the lack of open riverbanks and the increase in woody vegetation at potential nesting sites threatens the reproductive success of the KWS gharial population. This population persists today in a regulated river ecosystem, and nests in an altered riparian habitat which appears to be increasingly unsuitable for the continued successful recruitment of breeding adults. This second-ranking, critically endangered remnant population may have incurred an "extinction debt" by living in a reservoir that will lead to its eventual extirpation.