Flow regimes profoundly influence river organisms and ecosystem functions, but regulatory approaches often lack the scientific basis to support sustainable water allocation. In part, this reflects the challenge of understanding the ecological effects of flow variability over different temporal and spatial domains. Here, we use a process-based distributed hydrological model to simulate 23 years of natural flow regime in 100 target bioassessment sites across the Adige River network (NE Italy), and to identify typical nivo-glacial, nivo-pluvial, and pluvial reaches. We then applied spatial stream-network models (SSN) to investigate the relationships between hydrologic and macroinvertebrate metrics while accounting for network spatial autocorrelation and local habitat conditions. Macroinvertebrate metrics correlated most strongly with maximum, minimum and temporal variation in streamflow, but effects varied across flow regime types. For example: i) taxon richness appeared limited by high summer flows and high winter flows in nivo- glacial and pluvial streams, respectively; ii) invertebrate grazers increased proportionally with the annual coefficient of flow variation in nivo-glacial streams but tended to decline with flow variation in pluvial streams. SSN models revealed that most variation in macroinvertebrate metrics was accounted for by spatial autocorrelation, although local land use and water quality also affected benthic invertebrate communities, particularly at lower elevations. These findings highlight the importance of developing environmental flow management policies in ways that reflect specific hydro-ecological and land use contexts. Our analyses also illustrate the importance of spatially-explicit approaches that account for auto-correlation when quantifying flow-ecology relationships.