Alpine streams are among the most impacted freshwater ecosystems due to climate change. Depending on water origin, streams within alpine catchments are divided into glacier-fed, groundwater, and snowmelt streams. With the shrinking of glaciers due to climate change and higher temperatures along with decreasing snow coverage, it is predicted that glacier-fed streams will eventually be replaced by groundwater and precipitation-fed streams. This shift in water source will have profound effects on the physicochemical characteristics of stream water, such as the composition of organic matter, turbidity, conductivity, and patterns in discharge. Hence, direct effects are anticipated for the microbial communities and assemblages inhabiting these environments. To investigate these, we analyzed the microbial community and associated functionality via genome resolved metagenomics of three Swiss catchments by focusing on the differences between glacier-fed and groundwater stream types. While the main functions of the microbiome were conserved, we observed that the “groundwater” genomes were on average 20% longer than those significantly more present in glacier-fed streams. Consequently, much higher functional heterogeneities in groundwater genomes were found, mainly due to the numerous genes involved in the transport and degradation of organic matter along with resistance to antibiotics and heavy metals. These results suggest that the shift that glacier shrinkage will have with different water chemistry directly affected by hydrologic flow paths will have profound effects on the communities at a micro and macro scale.