The Saltwater Crocodile, Crocodylus porosus is endangered in Bangladesh, and currently surviving in rivers and channels of the Sundarbans mangrove forest of the country. Very little information is available on this apex predator in the Sundarbans aquatic ecosystem, therefore a survey was carried out to assess population status and their spatial distribution. By surveying approximately 351 km of rivers of the Bangladesh Sundarbans during daytime between 2014 and 2015, a total of 42 individual crocodiles were recorded, with an overall encounter rate of 0.12 crocodiles (SE = 0.02, 95% CI = 0.08 - 0.18) per km of rivers. Based on this estimate, it is inferred that a population of approximately 140 crocodiles (95% CI = 90 - 190) could occur in the Bangladesh Sundarbans. The generalised linear model revealed statistically insignificant negative relationship of relative crocodile abundance with the salinity level (β = –0.067, SE = 0.057, p = 0.242) and protection status (β = –0.208, SE = 0.855, p = 0.808), and statistically insignificant positive relationship with the distance to human habitations (β = 0.004, SE = 0.039, p = 0.914). Disturbance by resource collectors, cargo vessels, and water pollution are the major threats to crocodile populations of the Sundarbans. The results of this study will be useful in future population monitoring to guide conservation management of saltwater crocodile in this important habitat.