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Understanding the physical and biological mechanisms contributing to flow velocity–ecology relationships is crucial for successful river management. The application of an ecological traits‐based approach offers the potential to explore mechanistic linkages between aquatic communities and a hydrological gradient. To date, however, studies focused on identifying these relationships have been limited by a lack of large‐scale, long‐term biological data. To address this gap at a scale relevant for water policy management, we employed data from a large‐scale standardised benthic monitoring program—the Canadian Aquatic Biomonitoring Network—obtained from wadeable river sites across Canada. We applied the Threshold Indicator Taxa ANalysis method to quantify the response of the macroinvertebrate community, expressed as traditional taxonomic information and also as ecological traits, along a flow velocity gradient in reference and potential reference sites. Five key findings emerged: (1) using taxa and trait modalities revealed different flow velocity thresholds, (2) trait flow velocity indicators were less variable than taxon indicators, especially for positively responding trait modalities, (3) labile and non‐labile trait modalities demonstrated highly similar patterns along the flow velocity gradient, (4) taxa from 12 different orders responded negatively to flow velocity, while only EPT taxa and some dipterans responded positively to flow velocity, and (5) traits related to mobility and ecology (e.g. climber and swimmer habits, preference of cold‐cool eurythermal water and ability to survive desiccation) tended to respond positively to flow velocity, while traits related to morphology, life history and ecology (e.g. sprawler and burrower habits, preference for warm eurythermal water and inability to survive desiccation) tended to respond negatively to flow velocity. Providing ecologically based flow management targets can improve management plans, anticipate ecosystem consequences of anthropogenic change and support the development of policies to mitigate anthropogenic flow alteration. While our taxon and trait modality flow indicators were developed for Canadian watersheds, our methods to develop flow indicators and thresholds are transferrable to other systems where long‐term biomonitoring programs are being developed, underscoring the need for long‐term biomonitoring programs to support better ecosystem management.

Tidepools experience significant gradients in ecologically relevant physical variables along the transition from ocean to terrestrial habitat (vertical axis) and from open coast to inner bays (horizontal axis). Associations amongst physical and biological variables, divided into algal, invertebrate and vertebrate (fish) groups, were examined in a tidepool survey dataset. Physical variables and the three biological groups were submitted separately to a principal component analysis (PCA). PCA scores were evaluated with Pearson correlation coefficients across the sampling units (tidepools) to identify significant correlations. Initially little structure in the data and no correlation amongst variables was present. At the onset of summer, correlations were confined amongst physical variables and algal and invertebrate components, followed in the late summer with correlations between invertebrate and fish components. By the fall, correlations were confined to fish and algal/ invertebrate components. Species relationships followed a seasonal cycle with a succession from little to no structure, the forming of low trophic level relationships in the early summer to high trophic level relationships in late summer-fall, and deconstruction of structure with the onset of fall-winter storms and ice scour. The seasonal pattern, and well established vertical gradient, has nested within it species composition changes along a horizontal wave energy gradient. The horizontal gradient results in a shift from species which are physiologically adapted to extreme salinities and temperatures to those which are physically adapted to high wave-energy environments.

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