Stream bed and mid‐column velocities, depth, redox, and mussel densities were measured in 76 quadrats across five transects in Margaritifera margaritifera habitat supporting high densities of adult mussels and evidence of recent juvenile recruitment.At relatively low flow (Q85), the near‐bed velocities over the mussel habitat remained high, with optimal habitat having stream velocities of 0.27–0.31 m s−1.The average near‐bed velocity for mussel densities greater than 20 m−2 was 0.3 m s−1, with a range from 0.18 m s−1 for mussel densities lower than 10 m−2, to 0.3 m s−1 for mussel densities greater than 50 m−2.The average velocity at 60% depth for mussel densities greater than 20 m−2 was 0.37 m s−1, with a range from 0.21 m s−1 for mussel densities lower than 10 m−2, to 0.39 m s−1 for mussel densities greater than 50 m−2.Percentage redox losses from open water to water at 5 cm substrate depth were an average of 18% for mussel densities of 1–10 m−2 to 13% at mussel densities >100 m−2.The conclusion from this study is that relatively high velocities are present at relatively low flows in sustainable Margaritifera habitat, suggesting that this species is adapted to a combination of stable substrate conditions that are kept clean through high water velocities with low fine sediment infiltration, rather than habitat that is subject to regular fine sediment infiltration followed by substrate cleansing. Copyright © 2014 John Wiley & Sons, Ltd.