Deposition of gaseous compounds and nanoparticles from ship emissions was studied by micrometeorological methods at Harmaja in the Baltic Sea. The gradient method was used to measure fluxes of SO 2 , NO, NO 2 , O 3 , CO 2 , and N tot (number concentration of nanoparticles). In addition, the fluxes of CO 2 were measured by the eddy covariance method. Distortion of the flow field caused by obstacles around the measurement mast was studied by applying a computation fluid dynamic (CFD) model. This was used to establish the corresponding heights in the undisturbed stream, and the wind speed as well as the turbulent parameters at each of the established heights were recalculated for the gradient model. The effect of waves on the boundary layer was taken into consideration, because the Monin-Obukhov theory used to calculate the fluxes is not valid in the presence of swell. Uncertainty budgets for the measurement systems were constructed to judge the reliability of the results. No clear fluxes across the air-sea nor sea-air interface were observed for SO 2 , NO, NO 2 , NO x (= NO + NO 2 ) or O 3 , while a negative flux was observed for N tot with a median value of -0.23×10 9 m -2 s -1 and an uncertainty range of 31-41 %. For CO 2 , while both positive and negative fluxes were observed, the median value was -0.0036 mg m -2 s -1 with uncertainty ranges of 25-36 % and 30-60 % for the GR and EC methods, respectively. Ship emissions were responsible for deposition of Ntot while they had a minor effect on CO 2 deposition. The fuel sulfur content (FSC) of the marine fuel used in ships passing the site was determined from the observed ratio of SO 2 and CO 2 concentrations. A typical value of 0.40 ± 0.06 %, was obtained for FSC, which is in compliance with the contemporary FSC limit value of 1 % in the Baltic Sea Area. The method to estimate the uncertainty of FSC was found to be accurate enough for use with the latest regulations, 0.1 % (Baltic Sea Area) and 0.5 % (Global Oceans).