A method of assessing the mean eddy viscosity profile (EVP) in the sea surface boundary layer (SBL) under variable wind conditions is proposed. Performance of the method is tested using observations by an ADCP-equipped platform in the coastal environment of the northwestern Mediterranean Sea under variable (3–12 m s−1) wind conditions. EVP retrievals are made by a variational method strongly constrained by the Ekman dynamics, with the wind and velocity observations assumed to be uncertain within the prescribed error bars. Results demonstrate a reasonable agreement of the EVPs with KPP shape functions for stronger (8–12 m s−1) wind conditions and appear to be consistent with the classical Pacanowski–Philander parameterization of the viscosity profile based on the Richardson number. For weaker (3–5 m s−1) winds, the EVP retrievals turn out to be less accurate, which is primarily attributed to the decay of the wind-driven turbulence energy in the SBL. Feasibility and prospects of the retrieval technique are discussed in the context of uncertainties in the structure of the background flow and limitations of the microstructure and ADCP profiling.