The peat swamp forests (PSFs) of Sundaland, in Southeast Asia, support many endemic freshwater fish species. However, the future of these species is in doubt, owing to ongoing PSF deforestation. Here, we show that, if current rates of PSF conversion to a predominantly agricultural mosaic landscape continue through 2050, 16 fish species may become globally extinct. In the worst-case scenario, where the rate of conversion across the region matches that of the most rapidly deforested river basin, 77% (79 of 102 species) of the narrowly adapted (stenotopic) fish species are likely to become extinct, a figure that would more than double known extinctions of the world's freshwater fishes. As indicated by our analysis, the PSFs of Indonesia's Central Kalimantan region would be most severely impacted.