In alpine regions worldwide, climate change has induced unprecedented glacier shrinkage, and various stream ecosystems draining glacierized catchments are experiencing profound environmental changes. However, how microbial life in these streams will be affected remains poorly understood. We conducted a field-based, common garden experiment to study how glacier shrinkage may affect biofilm’s microbiome in glacier-fed and groundwater-fed streams’ sediment. This is relevant as melt waters may dominate runoff during glacier peak flow, while groundwater becomes more important beyond peak flow. We started biofilm growth in 30 flumes initially fed from a glacier-fed and groundwater-fed stream, mixing these waters (i.e., 0:100, 25:50, 50:50, 50:75 glacier: groundwater) along a source gradient once nascent biofilms had formed. We let biofilm develop in these treatments and compared their biomass (as chlorophyll-a, bacterial abundance) and community structure (16S rRNA and 18S rRNA genes) to the control (either 100% glacier- or groundwater-stream fed). We found that biofilm biomass increased with the influence of the groundwater-fed stream and that microbial diversity and turnover showed a gradual change along the source gradient. Our findings shed new light on the potential ecological trajectory of microbial life in rapidly changing alpine stream networks and provide a more unified understanding of the resilience potential of bacterial communities considering this transition.