Purpose In the Baltic Sea, the reduction of mercury load is estimated to be 44 % compared to the end of the previous century. Confirmation of mercury load decrease is frequently based on sedimentary mercury profiles. This study aims to assess the inter-annual changes of mercury concentration and the net input in surface sediments, in order to assess the effect of decreased emissions and other processes. Materials and methods Surface sediments were collected in 2011-2013 from areas where existing data series were available. Sediments were freeze dried, and total mercury concentrations, loss on ignition and fine fraction content were analysed. We compared recent concentrations of mercury in the coastal zone of the Baltic Sea to values previously reported in the same area since 1993. Net mercury deposition in the analysed sediments and previously reported data were calculated. The observed variability was correlated to climaterelated processes and input changes. Results and discussion Three studied areas-major river mouth, shallow bay and offshore area-were significantly different in terms of sediment type and mercury concentration. Total mercury concentrations in the study area in 2011-2013 ranged between 2 and 260 ng g −1 dry weight (dw) (mean 61 ng g −1 dw; median 36 ng g −1 dw). Nearly 75 % of the obtained results did not exceed 50 ng g −1 dw, while concentrations >200 ng g −1 dw accounted for a little over 5 % of all the obtained results. Mercury input calculated for the area was much smaller than that recorded for the 1990s, but was characterised with large inter-annual variability, attributed to climate-related processes.Conclusions Although a decreasing trend could be observed, it is modified by inter-annual variability. It follows from observations that in the present situation, where mercury emission has been successfully inhibited, that concentrations of this metal in sediments reflect natural metal migration processes rather than the direct influence of anthropogenic sources.