Acoustic Doppler current profilers (ADCP) are quasi-remote sensing instruments widely used in oceanography to measure velocity profiles continuously. One of the applications is the quantification of land–ocean exchange, which plays a key role in the global cycling of water, heat, and materials. This exchange mostly occurs through estuaries, lagoons, and bays. Studies on the subject thus require that observations of total volume or mass transport can be achieved. Alternatively, numerical modeling is needed for the computation of transport, which, however, also requires that the model is validated properly. Since flows across an estuary, lagoon, or bay are usually non-uniform and point measurements will not be sufficient, continuous measurements across a transect are desired but cannot be performed in the long run due to budget constraints. In this paper, we use a combination of short-term transect-based measurements from a vessel-mounted ADCP and relatively long-term point measurements from a moored ADCP at the bottom to obtain regression coefficients between the transport from the vessel-based observations and the depth-averaged velocity from the bottom-based observations. The method is applied to an Arctic lagoon by using an ADCP mounted on a buoyant platform towed by a small inflatable vessel and another ADCP mounted on a bottom deployed metal frame. The vessel-based measurements were performed continuously for nearly 5 h, which was sufficient to derive a linear regression between the datasets with an R2-value of 0.89. The regression coefficients were in turn applied to the entire time for the moored instrument measurements, which are used in the interpretation of the subtidal transport variations.