Current measurements in the open sea are generally acquired by Acoustic Doppler Current Profilers (ADCPs). In the case of ADCPs mounted on spar buoy, current profiles require to be post-processed, to properly take into account the buoy influence: in fact, ADCP compass may reflect alterations induced by the metal structure of the buoy and apparent currents can occur due to the large displacement of the platform. Uncertainty analysis is finally required to properly consider both these effects and to compute robust velocity estimates. A new methodology is tested for a measurement station in the Ligurian Sea, where an ADCP was mounted on the surface buoy of the W1-M3A (Western 1 Mediterranean Moored Multisensor Array) oceanographic observatory, facing upwards at the depth of about 40 m. Marine current numerical models and historical data in the area have been used as a basis for comparison to test the consistency of the proposed method. A very good agreement is obtained. Only minor discrepancies are reported (e.g., monthly averages from the reference model slightly underestimate the west-east current component along the entire profile), but, in general, the application of the proposed methodology ensures that the spar buoy-mounted ADCP system is able to provide reliable measurements for oceanographic studies and validation of 3D hydrodynamic models.