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1. We investigated the diversity and distribution of freshwater mussels at 40 sites in an agricultural catchment, the River Raisin in south-eastern Michigan, to relate mussel assemblages and individual taxa to reach and catchment-scale variables. Unionids were surveyed by timed searches in 100-m reaches, and in-stream and riparian habitat were quantified as well as flow, water chemistry and channel morphology. Land use/cover and surficial geology were determined for site subcatchments and riparian buffers. 2. Some 21 mussel species were found overall; richness ranged from 0 to 12 living species per site. From the upper to middle to lower catchment, the number of individuals, number of species, Shannon–Weaver diversity and relative abundance of intolerant unionids all declined significantly. 3. Four groupings based on overall mussel diversity and abundance were significantly related to reach-scale habitat variables. The richest mussel assemblages were associated with sites with higher overall habitat quality, greater flow stability, less fine substratum, and lower specific conductance. 4. Stepwise multiple regressions revealed that the distribution and abundance of the total mussel assemblage, as well as the most common species, could be predicted from a combination of reach- and catchment-scale variables ( R2 = 0.63 for total mussels, R2 = 0.51–0.86 for individual species). 5. Flow stability, substratum composition and overall reach habitat quality were the most commonly identified reach-scale variables, and measures of surficial geology were the most effective catchment-scale variables. The spatial pattern of geology is likely to be responsible for the diversity gradient from the upper to the lower catchment. 6. Prior studies, attempting to explain mussel distributions from local habitat features alone, have found relatively weak relationships. By employing a combination of reach- and catchment-scale habitat variables, this study was able to account for a substantial amount of the spatial variability in mussel distributions. [ABSTRACT FROM AUTHOR]