Although processes involved in the relationship between hyporheic and benthic zone have been elucidated in recent years, the spatial and temporal dynamics of the invertebrate assemblages is unclear in alpine streams. A field study was carried out in a glacier-fed stream and in its main spring-fed tributary, in the Italian Alps. Benthic hyporheic connectivity was investigated by means of a pond net, a pump, and artificial substrates. The main determinant in structuring the community was the habitat (=benthic, hyporheic), accounting for 22% of the total faunal variation. A strong similarity was detected between the two streams in structure, function, and species seasonal variations of the hyporheos, that was, in both, more species rich than the benthos. In contrast, benthos was generally very different between the two streams, with a more pronounced turnover in the glacier-fed than in the spring-fed stream. Overall, the highly disturbed glacial system hosted a simplified benthos and hyporheos compared to the stable spring system, in agreement with the intermediate disturbance hypothesis. Our findings provided also evidences about the trophic-sink effect between benthos and hyporheos. Spatial connectivity that we highlighted might have a key role in the dispersal of invertebrates facing changes in habitats features due to climate change.