Summary1. Longitudinal changes in physicochemical factors and the composition of the invertebrate community were examined in the hyporheic zone of a glacial river (Val Roseg, Switzerland) over a distance of 11 km from the glacier terminus. Multivariate analysis was used to determine the habitat preferences of taxa along an upstream‐downstream gradient of increasing temperature and groundwater contribution to river flow.2. The hyporheos conformed to the longitudinal distribution model described for zoobenthic communities of glacial rivers in that taxonomic richness increased with distance from the glacier terminus. Spatial variation in taxonomic richness was best explained by temperature, the influence of groundwater, and the amount of organic matter. The overriding importance of these variables on the distribution of taxa was confirmed by the multivariate analysis.3. The hyporheic zone contributed significantly to the overall biodiversity of the Roseg River. Whereas insect larvae were predominant in the benthos, hyporheic invertebrates were dominated by taxa belonging to the true groundwater fauna and the permanent hyporheos. Several permanently aquatic taxa (e.g. Nematoda, Ostracoda, Cyclopoida, Harpacticoida, Oligochaeta) appeared exclusively in the hyporheic zone or they extended farther upstream in the hyporheic layer than in the benthic layer. Leuctridae, Nemouridae, and Heptageniidae colonised hyporheic sediments where maximum water temperature was only 4 °C.4. Despite strong seasonal changes in river discharge and physicochemistry in hyporheic water, the density and distribution of the hyporheos varied little over time.5. Taxonomic richness increased markedly in the downstream part of a floodplain reach with an extensive upwelling zone. Upwelling groundwater not only maintained a permanent flow of water but also created several species‐rich habitats that added many species to the community of the main channel.