Since the '70s, the ENEA Marine Environment Research Centre of S. Teresa has been involved in monitoring and analysis of physical, chemical and biological processes in marine environment. In order to provide a deeper view of the real marine dynamics, based on the integrated use of data and models, some of these activities have been recently focused on the measurement of current profiles in the open sea. A dedicated experimental methodology and data analysis were carried out to design and install a system for measuring current profiles in the surface layer in the Ligurian Sea: the measurement station, based on an Acoustic Doppler Current Profiler (ADCP) mounted on the surface buoy of W1-M3A (Western 1 Mediterranean Moored Multisensor) weather-oceanographic observatory, led to the acquisition of a time series of data continuously acquired for five months (from April to August 2017). The collected dataset, together with the implemented post-processing techniques, were aimed to realize a monitoring system able to support (and verify by comparison) marine current numerical models, with the final purpose of improving their performances. Main object of this work are both the correction of bias effects due to the buoy influence on ADCP measures and the evaluation of the overall uncertainty associated with the current velocities. In the following, an overall view of the performed experimental activity is briefly reported, ranging from the design of the measuring station to its implementation, from recovery to preliminary data processing and uncertainty analysis applied to a sub-set of data, used as a test case.