Sitatunga is a rare semi-aquatic antelope inhabiting wetlands and swampy environments in northern Botswana. This makes it to be vulnerable to variability in wetlands inundation extent and projected changes in climate. Given the projected global climate change over Southern Africa, it is essential to first interrogate available data on Sitatunga population and associated inundation levels in an effort to avail baseline data to be used for forecasting the behavior of Sitatunga populations and distribution over the next 20 years. Regression statistics was applied to analyse wildlife population aerial census data from 1992 to 2012 and 8 decades river flow data. Optimized hotspot analysis of Sitatunga sightings from 1991 to 2013 was also performed and mapped in ArcGIS. The results revealed a steady decrease in Sitatunga populations since 1991 from over 2233 individuals to 63 animals in 2012. Based on hotspot analysis results, it was discovered that Jao area and its environs covering NG24 is the Sitatunga sighting hotspot in the Okavango Delta. The decline in Sitatunga population is regarded as a lag response of this species to decrease in inundation level from 1985 to 1995. Therefore, Sitatunga population is vulnerable to potential climate change extreme events. Policy interventions and mitigation strategies are essential to conserve the species through establishment of Sitatunga dispersal corridor in its prime habitats.