Climate change is expected to affect freshwater water bodies worldwide, especially those located in semiarid and arid regions, including the Arabian Peninsula. Species distribution modeling has been widely used to predict the effects of climate changes on aquatic species. Occurrence records of the cichlid fish Nile tilapia, Oreochromis niloticus, were geographically mapped, followed by the implementation of species distribution models to delineate its range within the sensitive inland water system of the southeastern Arabian Peninsula. The analysis encompassed the examination of species presence data in the context of environmental variables, leading to the development of an ensemble model for habitat suitability, combining four distinct species distribution models. The findings indicated that the mean diurnal range and precipitation seasonality emerged as the most influential factors in predicting the suitability of habitats for O. niloticus. The response curve analysis indicated that the presence probability of O. niloticus decreased with increasing mean diurnal range and decreasing precipitation seasonality. The suitable distribution ranges for O. niloticus in the studied area were mainly distributed in the northeast of this region, where native/endemic fish diversity is high. The ensemble model results specified a significant impact of climate change on O. niloticus distribution, so highly suitable areas for this species will be reduced, while areas with low to moderate suitability increase slightly or remain unchanged. While O. niloticus is anticipated to display resilience and prosper under the influence of climate change, it remains paradoxical that its habitats are at risk of being compromised by climate-induced alterations. Consequently, even this resilient species stands susceptible to the repercussions of climate change. Due to the worldwide severe impacts of Nile tilapia, regular monitoring of freshwater ecosystems and fish fauna—especially in the northeast of the Arabian Peninsula, which has currently been invaded by this alien species—and protecting the region from key anthropogenic stressors are recommended to successfully conserve the freshwater fishes, which include about 22 recognized fish species in 16 genera, 10 families, 7 orders, and a class including 20 natives (7 endemic) species, out of which 13 species co-occur in sympatricity with O. niloticus.