Deglaciation in mountain catchments changes water source contributions and associated habitat conditions in usually cold and dynamic mountain rivers. Although recent research has listed consequences of glacier retreat for aquatic biodiversity, specific invertebrate and algal groups, quantitative effects on the aquatic food web structure remain poorly understood. In this study we assessed abiotic habitat conditions together with the composition and the biomass of periphyton in 5 catchments in the Central European Alps over the snow-free period and reveal significant links to declining glacier cover. We found that reduced glaciation leads to decreasing sediment concentrations and also to lower runoff, which in combination affects the stability of benthic habitats. The reduced sediment load of the rivers dominates the consequences of glacial retreat in subsequent river habitats more than the decreasing nutrient supply. Periphyton biomass in glacier-fed rivers is expected to increase with ongoing deglaciation and warming, which subsequently favors particularly diatoms and cyanobacteria. This work thus illustrates clear links between decreasing glacier cover and the identity and relevance of aquatic producers in alpine river catchments, and provides evidence for shifting resource base in terms of biomass with potential consequences for its nutritional quality.