The gharial Gavialis gangeticus is a Critically Endangered crocodilian endemic to the Indian subcontinent. Habitat modification by river damming and water extraction has caused a severe decline in its population. The status of the gharial is known within protected areas, but there have been few surveys for this species in unprotected areas. In Katerniaghat Wildlife Sanctuary, a breeding gharial population in Girijapuri Barrage Reservoir has low recruitment, and it has been hypothesized that yearlings disperse downstream into the unprotected Ghaghara River when the barrage gates are opened. We surveyed a 100-km stretch of the Ghaghara River from the Girijapuri Barrage to Chahlari Ghat, observing a total of 84 gharials, including a high proportion of juveniles. A survey in 2021 from Chahlari Ghat to Ayodhya observed 174 gharials, giving a combined total of 258 gharials in a 219-km stretch of the Ghaghara River for the two surveys. Together, these findings confirm the presence of a significant population of gharials in the Ghaghara River. We recommend the adoption of an integrated approach, involving government agencies and local communities along the river, to conserve the protected Girwa–Kaudiyala Rivers and the unprotected Ghaghara River for gharial conservation and recovery. Such a programme will need to tackle the threats facing the gharial and establish baseline data and long-term monitoring protocols for freshwater species conservation in this river system.