Fine-scale measurements of boundary layer flow and solute transport were conducted within a laboratory flume to determine how bed topography influences mixing and mass transport at the sediment-water interface. Three different bed topographies were examined, with roughness composed of sand, gravel, or cobbles. Fluorescein dye, used as a dissolved tracer, was injected into the flow, and concentration and velocity were simultaneously measured using a combined planar laser-induced fluorescence and particle image velocimetry technique. Enhanced turbulent mixing due to bed roughness increased mass flux across the sediment-water interface between 1.3 times greater for the sand and 7.5 times greater for the cobble bed compared to estimates over a hydraulically smooth surface. As bed roughness increased, mass exchange became spatially more heterogeneous, coinciding with a transition from a boundary layer to a shear-dominated mixing layer in the near-wake region behind individual roughness elements. The enhanced flux increased pore water concentrations. However, for the same bed geometry, increased mean flow within the water column locally reduced pore water concentrations, likely due to greater downstream transport and dispersion occurring within the bed.