The Atrato slider Trachemys medemi is a freshwater turtle endemic to the Atrato River basin in the Urabá region of north-west Colombia. Although there is limited information about the species, it was provisionally categorized as Vulnerable on the IUCN Red List by the IUCN Turtle Taxonomy Working Group in 2021 because of its restricted distribution. This study aimed to estimate the potential distribution of T. medemi, identify relevant climatic factors affecting its geographical range and predict its probable future distribution under different climate change scenarios. We recorded its occurrence along the Atrato River and in the surrounding areas, and we employed an ecological niche modelling approach to predict species distribution based on our field data and literature records. Our model indicated that the aquatic distribution of the Atrato slider encompassed the lower, middle and upper Atrato River. This distribution was influenced by air temperature, water temperature and hydrological slope. Our climate change models predicted a dramatic loss of suitable habitat in future, leading to > 50% reduction in T. medemi populations within 30 years. Considering the threat from climate change together with the cultural tradition of harvesting wild turtles for human consumption, we suggest (1) a conservation focus on areas of potential habitat already protected under the National System of Protected Areas in Colombia, (2) empowering local community-based programmes that protect biodiversity, and (3) encouraging reforestation to improve connectivity amongst habitats in the turtle’s geographical range, particularly in degraded areas.