Nepal initiated numerous hydropower and irrigation‐related infrastructure projects to enhance and promote green energy, water security, and agricultural productivity. However, these projects may pose risks to natural habitats and the well‐being of aquatic fauna, leading to significant effects on delicate ecosystems. To understand these potential impacts, it is crucial to gather reliable baseline data on the population status and habitat characteristics of species. This study specifically focuses on Gharials (Gavialis gangeticus), a critically endangered species. We recorded data on pre‐determined habitat variables at stations spaced 500 m apart along the two major river streams of Bardia National Park, as well as at locations where Gharials were sighted between February and March 2023. We used binary logistic regression with a logit link function to investigate the habitat characteristics related to the occurrence of Gharials. The presence/absence of Gharials at sampling points served as the dependent variable, while 10 other predetermined variables (ecological variables and disturbance variables) served as independent variables. Our study recorded 23 Gharials, comprising 14 adults, six sub‐adults, and three juveniles, with a sex ratio of 55.56 males per 100 females. Most individuals (83%) were found basking. Among the 10 habitat predictors, three variables (mid‐river depth, river width, and water temperature) were significantly correlated (p < .05) with the probability of Gharial occurrence. The model shows that Gharial detection probability increases with greater mid‐river depth and width and lower water temperature. This study establishes a population baseline for Gharials within the river system before the construction of large infrastructure projects, such as dams and irrigation canals. It also recommends continuous monitoring of Gharial populations after water release and/or diversion to evaluate the impact of large infrastructure projects on the population and their associated habitat characteristics. This will help enable more informed and targeted conservation efforts.