River channel confluences play a major role in the dynamics of all fluvial systems, and yet our understanding of bed load routing at these sites is very sparse. The dynamics of confluences are a function of the momentum ratio between the combining flows and the three-dimensional geometry of the junction. Recent experiments have shown that discordance in bed height between the confluent rivers increases turbulence intensity and enhances upwelling of flow within the confluence. However, the significance of these flow characteristics on sediment transport is still unknown. To examine the relations between flow and sediment transport, we have measured near-bed flow turbulence, bed load transport rates, and changes in bed morphology for eight different flow conditions at a sand bed discordant confluence. Detailed analysis of the near-bed flow patterns reveals that within the shear layer, low mean flow velocities are combined with the highest values of Reynolds shear stresses and that turbulence generation is associated with intense upward movements of flow. High sediment transport rates are found at the edges of the shear layer region where horizontal-vertical cross stresses (ρUw′) are high. These patterns match changes in bed morphology where erosion occurs along the shear layer. The relation between the shear layer and sediment transport confirms the role of bed discordance on the dynamics of the confluence. Migration of the shear layer into the confluence, as a result of a change in momentum ratio, modifies local near-bed flow characteristics, sediment transport rates, and the spatial distribution of deposition and erosion zones.