Environmental radioactivity can act as a chronic stressor not only in nuclear accident zones but also in ecosystems that capture atmospheric pollutants, yet its effects on organisms remain understudied. Using biologically active glacier sediments that concentrate natural and legacy radionuclides, this study provides the ecosystem‑scale test of how chronic radiation affects microbial life outside nuclear accident zones. Across a radioactivity gradient, higher levels corresponded to significant declines in microbial richness and phylogenetic diversity. Functional diversity decreased, with fewer KEGG Orthologs, indicating elevated radioactivity as a selection factor. However, showing strong redundancy in this ecosystem, as key functions remain in the higher radioactive habitat. Despite stable overall functional profiles, an essential DNA repair pathway (non-homologous end joining) was enriched. Metatranscriptomic revealed significant metabolisms and growth suppression, shown by reduced RNA transcripts per DNA copy for metabolisms pathways. These results show that chronic environmental radiation is a strong, underrecognized ecological factor that decreases the biodiversity of glaciers threatened by climate change.