At tidal inlets, large amounts of water are exchanged with the adjacent sea during the tidal cycle. The residual flows, the net effect of ebb and flood, are generally small compared with the gross flux; they vary in magnitude and sign from one tidal period to the other; and their long-term mean varies from year to year. Here, we focus on the temporal variability of the residual flows in the Marsdiep tidal inlet, which is the western-most inlet of the Wadden Sea, a tidal lagoon along the coasts of the Netherlands, Germany, and Denmark. We compare the transport from a high-resolution numerical model with the transport from velocity profile data collected beneath a ferry that crosses the inlet daily. The comparison works in two ways: for the areas and times covered by the measurements, the data serve to validate the model, and conversely, the model is employed to assess the consequences of spatial and temporal gaps in the data. Modeled and observed transports over the region of the flow that is covered by the acoustic Doppler current profiler are in good agreement for gross and residual quantities. Results indicate that uncertainties due to spatial gaps can be overcome with a simple extrapolation approach applied to the velocity profiles, whereas uncertainties due to temporal gaps are more problematic and leave large discrepancies in the residuals.