Climate change is altering the structure and functioning of river ecosystems worldwide. In mountain rivers, glacier retreat has been shown to result in systematic changes in aquatic invertebrate biodiversity, but the effects of ice loss on other biological taxa and on whole-ecosystem functions are less well understood. Using data from mountain rivers spanning six countries on four continents, we show that decreasing glacier cover leads to consistent fungal-driven increases in the decomposition rate of cellulose, the world’s most abundant organic polymer. Cellulose decomposition rates were associated with greater abundance of aquatic fungi and the fungal cellulose-degrading Cellobiohydrolase I (cbhI) gene, illustrating the potential for predicting ecosystem-level functions from gene-level data. Clear associations between fungal genes, populations and communities and ecosystem functioning in mountain rivers indicate that ongoing global decreases in glacier cover can be expected to change vital ecosystem functions, including carbon cycle processes.