Climate change‐induced glacier retreat leads to the reorganization of fluvial landscapes in proglacial terrains and transitions between streams fed predominantly by glacial meltwater and groundwater. To explore the effects of such ecosystem transitions on benthic biofilm communities, we gradually mixed water from a glacier‐fed stream (GFS) and a groundwater‐fed stream (GWS) in 30 stream‐side flume mesocosms. Over 70 days, we studied how microbial biomass and community composition responded to changes in water sources compared to the respective controls. Biofilms responded readily to shifting water sources, with increased algal and bacterial biomass as GFS influence diminished, supporting previous reports of GFS “greening” as glacial influence is reduced. Bacterial community composition exhibited rapid and sensitive responses to the gradual transition between GFS and GWS, with an observed convergence between communities receiving the same water mixture. Partitioning temporal changes in bacterial communities revealed that increases in taxa abundance primarily underly compositional responses, indicating that taxa present in both stream types respond to changes. Piecewise Structural Equation Models suggest that changes in water source directly (through changes in nutrient availability) and indirectly (through benthic algal biomass) drive the observed compositional responses. Our experimental insights provide evidence for the “greening” of proglacial streams and shed new light on the sensitivity of benthic microbial communities to ecosystem transitions in proglacial floodplains.