Abstract Freshwater fishes are facing considerable threats in the Arabian Peninsula which is considered as a highly stressed region in the Middle East. It is predicted that northern Oman is likely to face decreasing rainfall and increasing temperature in coming decades. In this study, we focused on an endemic cyprinid fish Cyprinion muscatense, as a model to investigate impacts of climate change on the mountain fishes inhibiting in this arid region. This species is expected to be strongly affected by climate change because of its limited distribution range in a montane area surrounded by lowlands and sea, limiting the species in shift to other areas. We used an ensemble approach by considering two regressions‐based species distribution modeling (SDM) algorithms: generalized linear models (GLM), and generalized additive models (GAM) to model the species habitat suitability and predict the impacts of climate change on the species habitat suitability. Based on the distribution models, the montane area located in northeastern Oman was identified as the most suitable habitat for this species. Our results indicate that, even under the minimum greenhouse gas emissions scenario (RCP 2.6), climate change will produce a high reduction in its potential future habitats. According to the results of percent contribution, elevation and annual minimum temperature were the most important variables in predicting the species suitable habitats. Results also showed that only a small percentage of suitable habitats for the species within boundaries of protected areas. Therefore, the impact of climate change on the species appears particularly alarming. Although our study was restricted to a single cyprinid freshwater species, decreases in potential habitats are likely predicted for other cyprinid fish species restricted to the mountains of this region, suggesting severe consideration is needed for aquatic systems in future conservation planning, especially for endemic freshwater fishes.