Submerged vegetation creates a zone of slow flow close to the bed, which may enhance nutrient and sediment retention. The velocity within the canopy is diminished in proportion to the canopy density. Above the canopy, the flow profile is logarithmic. The abrupt change in hydraulic resistance at the top of the canopy creates a region of strong shear, which in turn generates coherent turbulent structures that scale with the canopy height. The canopy-scale vortices control the vertical exchange of mass and momentum between the canopy and the overflowing water. The penetration of the vortices into the canopy varies with planting density and blade stiffness. If the vortices cannot penetrate the full canopy height, the canopy is divided into two distinct regions. The upper canopy is flushed rapidly by the canopy-scale turbulence. The lower canopy is flushed more slowly, because only stem-scale turbulence exists in this region. The time scale for retention within a submerged canopy can be predicted by considering these two regions of transport. The retention times range from minutes to an hour, which is comparable with retention times for small hyporheic regions, such as sand bed forms and gravel bars. This suggests that the contribution of macrophytes to hydrologic storage should be considered.