Viruses are well known to modulate the biomass, diversity and activity of microbial communities in many ecosystems. Yet, little remains known about their role in stream biofilms. Here, we leverage metagenomic data from sediment biofilms in 200 glacier-fed streams (GFS) around the world to unravel the diversity and biogeography of benthic dsDNA viral communities. These environments are expected to harbour a high degree of viral novelty due to undersampling. This consideration motivated the development of a reference- independent bioinformatics pipeline for viral detection. Our new pipeline roughly doubles the number of putative viruses identified from metagenomic data, shedding new light onto viral dark matter in GFS. Among the 5000 high-quality viruses identified, almost none of them is found in public viral databases of isolates or metagenomic sequences, confirming the specificity to GFS. As observed for the host communities, most viral populations are sample-specific and only few are observed across all mountain ranges. Nonetheless, clustering by mountain ranges shows strong biogeographical signatures. The GFS microbiome is characterized by low cell abundances and few but well-adapted bacterial clades, likely reflecting adaptation to the extreme environmental conditions in these habitats. Among phages, it manifests as high host specificity and the encoding of auxiliary metabolic genes that mediate interactions with their hosts, pointing to the prevalence of mutualistic interactions rather than mere lysis of host cells in GFS. Similarly, a comparison of upstream and downstream samples reveals lower viral diversity near the glacier snout but a broader gene repertoire. Taken together, our work highlights the co-evolutionary history of phages and their hosts in a cryospheric ecosystem, now threatened by climate change.