Inland standing waters are particularly vulnerable to increasing water temperature. Here, using a high-resolution numerical model, we find that the velocity of climate change in the surface of inland standing waters globally was 3.5 ± 2.3 km per decade from 1861 to 2005, which is similar to, or lower than, rates of active dispersal of some motile species. However, from 2006 to 2099, the velocity of climate change will increase to 8.7 ± 5.5 km per decade under a low-emission pathway such as Representative Concentration Pathway (RCP) 2.6 or 57.0 ± 17.0 km per decade under a high-emission pathway such as RCP 8.5, meaning that the thermal habitat in inland standing waters will move faster than the ability of some species to disperse to cooler areas. The fragmented distribution of standing waters in a landscape will restrict redistribution, even for species with high dispersal ability, so that the negative consequences of rapid warming for freshwater species are likely to be much greater than in terrestrial and marine realms.