Tortoises and freshwater turtles are among the most threatened taxa of vertebrates in the world due to consumption, urban development, agriculture, and land and water pollution. About 50% of the currently recognised chelonian species are considered threatened with extinction according to the IUCN Red List. Asia is an epicentre for the turtle and tortoise extinction crisis, containing the highest diversity of threatened species. In this study, we used species distribution models (SDMs) to assess the effectiveness of existing protected areas across Southeast and South Asia for the conservation of three large critically endangered freshwater turtles (Batagur borneoensis, B. affinis, and Pelochelys cantorii). We derived the models based on selected bioclimatic variables at the sites of known species records. Our SDMs showed that Indonesia is of particular importance in prioritising conservation for these three species, containing the largest areas of suitable habitat within protected areas. However, when considering water surface coverage, Thailand has the highest proportion of suitable areas under protection. Our results suggest that the present cover of protected network reserves seems inadequate in terms of size and should be expanded to sustain populations of the three target species. Therefore, we identified priority areas and reserves critical for further field surveys to guide the potential discovery of novel populations. To investigate the effect of climate change, we also projected potential distributions onto ensembles of four IPCC story lines. As a result, we found larger extralimital areas of suitable environment for all three species, particularly northwards and inland. However, high degrees of uncertainty in climate conditions indicate few reserves may provide long term protection. Lastly, we review the threats and propose recommendations for conservation of these poorly known freshwater turtles.