As glaciers shrink, new terrain is exposed and drained by proglacial streams along both longitudinal and lateral chronosequences which are fed by various water sources (glacier melt, snowmelt, and groundwater). While benthic microbial biofilms often initiate primary succession towards more complex ecological communities in these nascent streams, it is unclear how their microbial communities are assembled. Given the extreme environments in pro-glacial streams (cold temperatures, high ultra-violet radiation, etc.), we expect strong deterministic processes (e.g., selection) to dominate community assembly in both glacier-fed and groundwater streams. However, we expect that taxa under strong selection pressure will differ between glacier-fed and groundwater streams according to their respective environmental condition. To test this, we sampled three glacial floodplains in Switzerland over two seasons (early and late glacier melt season) and sequenced the 16S rRNA genes from more than 260 sediment samples. We used compositional and phylogenetic turnover patterns as well as phyloscore analysies to identify the dominant processes and taxa under the influence of these processes, respectively. Overall, we found that the dominant assembly process was homogeneous selection across all streams and that low phylogenetic turnover is driven by different clades in the two different stream types. Indeed, Gammaproteobacteria clades were selected in glacier-fed streams while Alphaproteobacteria and Patescibacteria clades were found in groundwater-fed streams. Our findings shed new light on the presence of fine-scale phylogenetic architecture and its consequences for the success of microbial life in the streams draining proglacial floodplains.