The vertical structure of the along-stream current in the main channel of the periodically-stratified estuarine Marsdiep basin is investigated by combining velocity measurements collected during three different seasons with a one-dimensional water column model. The observed vertical shears in the lowest part of the water column are greater during ebb than during flood due to an asymmetry in drag coefficient (i.e. bed friction), which is most likely determined by the surrounding complex bathymetry. This asymmetry is usually not incorporated in models. Furthermore, a mid-depth velocity maximum is observed and simulated during early and late flood which is generated by along-stream and cross-stream tidal straining, respectively. Negative shears are present in the upper part of the water column during flood, which correlate well with the along-stream salinity gradient. The mid-depth velocity maximum during late flood results in an early current reversal in the upper part of the water column. The elevated vertical shears during ebb are able to reduce vertical stratification induced by along-stream tidal straining, whereas cross-stream tidal straining during late flood promotes the generation of vertical stratification. The simulations suggest that these processes are most important during spring tide conditions. This study has demonstrated that an asymmetry in bed friction and the presence of density gradients both have a strong impact on the vertical structure of along-stream velocity in the Marsdiep basin