High-mountain streams are particularly vulnerable to climate change because they intimately interface with the cryosphere. As glaciers shrink and snowpack diminishes, proglacial streams will eventually shift from being glacier-fed to streams fed by groundwater, snowmelt and precipitation. This shift will affect both the flow regime and physico-chemical characteristics of streams, possibly also the structure and function of their benthic microbiome. Here, we applied genome-resolved metagenomics to benthic biofilms from glacier-fed streams and their groundwater-fed tributaries within three proglacial floodplains in the Swiss Alps. Despite the close spatial proximity between both stream types, their microbiome structure differed consistently for both prokaryotes and eukaryotes. The glacier-fed stream microbiome was taxonomically and functionally less diverse than its groundwater-fed counterpart, and had smaller genomes, but with conservation of the central metabolic functions primarily related to nitrogen and sulfur cycling. Consequently, much higher functional variability was associated with the microbiome of tributary streams, mainly due to abundant genes involved in the transport and degradation of organic matter. Our findings suggest that glacier shrinkage will cause shifts in the functioning of benthic microbiomes of proglacial floodplains with yet unknown consequences for downstream biogeochemistry.