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Freshwater mussels are dominant ecosystem engineers in many streams throughout North America, yet they remain among the world's most imperiled fauna. Extensive research has quantified the ecological role of mussels in aquatic habitats, but little is known about the interaction between mussels and their surrounding physical and hydrodynamic habitat. Here the physical interactions of mussels with near‐bed flow are investigated in an experimental channel using model mussels. The results show that (1) mussels disrupt the distributions and magnitudes of time‐averaged values of longitudinal flow velocity and Reynolds shear stress depending on mussel density, and (2) at densities of approximately 25 mussels m⁻²and greater, a hydrodynamic transition occurs where the maximum Reynolds shear stress is displaced from the bed to the height of the mussel canopy, near‐bed longitudinal flow velocity is reduced, and average turbulent shear stresses acting on the mussels are reduced by as much as 64%, thus markedly decreasing the dislodgement potential of the mussels by these stresses. These results provide strong empirical evidence for a positive density‐dependent effect related to flow‐organism interactions and their ecological success, such as enhancing river bed hydrodynamic habitat complexity or decreasing the turbulent shear stresses acting to dislodge mussels from the river bed. This information will improve the understanding of the long‐term persistence of mussel beds and help focus future conservation strategies.