Ongoing glacial retreat is expected to lead to numerous changes in glacier-fed rivers. This study documents the development of community composition of the hitherto widely neglected micro- and meiobenthos (MMB: bacteria, fungi, algae, protists, and meiofauna) in glacier rivers in response to the distinct habitat conditions driven by different stages of (de)glacierization. Our model is based on the glacier catchments of the Möll River (MC) and Kleinelendbach stream (KC), in the Austrian Alps, with 60% and 25% glacierization and glacier retreats of 403 and 26 m, respectively, since 1998. Analyses of overall catchment diversity and resemblance patterns showed that neither intense glacierization nor rapid deglacierization were predominant MMB determinants. This was ascribed to the specific environmental conditions at the MC, where the rapidly retreating Pasterze glacier has formed a harsh unstable proglacial, but also a benign floodplain area, with the former suppressing and the latter supporting the structural development of the MMB. Comparisons of similarly aged riverine habitats of the MC proglacial and the KC main channel further evidenced developmental suppression of the MMB (64 taxa) by the rapidly retreating MC glacier, unlike the moderate glacial retreat in the KC (130 taxa). Habitat conditions interacting with melt periods explained the differences in MMB resemblance patterns, which themselves differentially reflected the spatiotemporal habitat settings imposed by the different glacier activities. The varying glacial influences were represented by a glaciality index (GIm) based on water temperature, electrical conductivity, and stream bed stability. The taxonomic richness of nematodes, rotifers, algae, and diatoms was distinctly related to this index, as were most MMB abundances. However, the strongest relationships to the GIm were those of nematode abundances and maturity. Our observations highlight the intense response of the MMB to ongoing glacier retreat and the utility of a simple index to reveal such patterns.