The gharial is a critically endangered freshwater crocodylian. Research on gharials in Chitwan National Park has predominantly focused on the Rapti River; however, the Narayani River also harbors a significant potential habitat. This study assessed habitat factors associated with gharial occurrences and conservation threats along the Narayani River. In March 2022, we conducted a boat-based daylight survey within a 50-km segment of the Narayani River. We assessed the habitat characteristics at stations spaced at 500 m intervals along the river and wherever we spotted gharials. We analyzed the habitat factors influencing the gharial occurrence using binomial logistic regression. We conducted a threat survey, interviewing 155 Narayani river-dependent households within 1 km of the riverbank. We gathered local knowledge of gharial threats in the study area and later analyzed it to identify the perceived major anthropogenic threats to gharials. We detected 33 gharials in total, with an encounter rate of 0.66 gharials per km. Only two of the 10 habitat variables examined, river water depth and water temperature, showed significant associations in gharial habitat selection. Most of the gharials were detected at 2-3 m of water depth and 19 ˚C of water temperature. Although not statistically significant, most of the individuals were sighted when there was 25˚- 30˚C air temperature, river width of 200-300 m, on sandy riverbanks with a flat topography and riverbank slope of 0-30˚. Similarly, a greater proportion of observations occurred in locations with no invasive alien plant species and no observed anthropogenic threats. People perceived gillnet fishing, dam impact, and human disturbances as major anthropogenic threats to gharials and their habitat. Moreover, people perceived gillnet fishing, dam impacts, and human disturbances as major anthropogenic threats to gharials and their habitat. We highly recommend preserving river confluences, maintaining sandbanks, and eliminating the use of gillnets.