Linking hydromorphological diversity to biodiversity and functioning in running waters

Environmental heterogeneity is a key driver of biodiversity and ecosystem functioning, yet linking physical habitat variability to ecological attributes remains challenging in aquatic ecosystems. Here, we present a unified framework that applies variance partitioning to hydromorphological characteristics—specifically flow velocity and depth—to quantify habitat heterogeneity across spatial and temporal scales. Drawing on field data from two gravel‐bed streams, we decompose physical variability into α (local), β (between habitat), and γ (total) components and relate these to the diversity of microbial biofilms and nitrogen uptake. We find that β diversity—representing spatial variability among mesohabitats—dominates both hydromorphological and biological γ diversity. The diversity of autotrophs and phagotrophic protists increased significantly with flow β diversity, whereas bacterial diversity was unresponsive to flow heterogeneity. Functional diversity, measured as spatial variability in nitrogen uptake efficiency, also increased with flow β diversity but was unrelated to local turbulence ( α diversity). These findings highlight the central role of habitat‐scale flow structure in shaping biodiversity and function in stream ecosystems. The proposed physically grounded, scale‐explicit framework provides a transferable tool for assessing ecological responses to habitat heterogeneity and offers a quantitative basis for guiding restoration and conservation.