Global climate change produces important shifts in the glacial runoff, modifying the relative contributions of meltwater and glacial clay discharges into headwater streams. Physical and chemical factors of glacier-fed streams are affected, such as total suspended solids (TSS), and nutrient concentrations. Here, we analyze the composition of the biofilm bacterial community by 16S rRNA sequencing along a glacier-fed network (Upper Rio Manso) located in North Patagonian Andes (Argentina). We also analyzed changes in environmental factors in relation to the bacteria composition in different seasons (spring, summer, and autumn). Our results showed that the dominant phyla were Proteobacteria, Cyanobacteria, Bacteroidota, Actinobacteriota, and Acidobacteriota. Bacterial community composition changes longitudinally and seasonally in relation to glacial influence (TSS and phosphorus concentrations). We identified phylotypes of Proteobacteria (Polaromonas, Rhodoferax, and Methylotenera) that were only present in headwaters of the fluvial systems. In addition, Cyanobacteria also presented substantial changes along the main course of Manso River and among seasons. The increase of Cyanobacteria abundance was favored by the glacial influence both longitudinally and seasonally. Overall our results contribute to the understanding of the patterns of biodiversity and bacterial composition under a constant glacial retreat.