Rivers represent the main source of mercury (Hg) in the Southern Baltic. Nevertheless, the concentration and proportion of individual Hg forms in rivers depend on the management of the river basin, as well as on the intensity of meteorological phenomena. Hence the aim of the present study was to determine the influence of drought and rains/intense rains on the content of labile and stable Hg forms in the soil of river catchments with various types of land management, and on the inflow of bioavailable mercury to the coastal zone of the sea. Soil and sediment samples were taken from two rivers flowing into Puck Bay (Southern Baltic): the Reda and Gizdepka. In order to determine Hg concentration and the proportions of its particular forms in the collected material, the thermo-desorption method was used. Five periods were identified during which the soil was enriched with various Hg forms. The obtained results showed that in periods of intensive development of vegetation, the soil becomes enriched with absorbed mercury (Hg). On the other hand, as a result of Hg emissions during the heating of buildings, mercury associated with halides (Hg) is deposited on land, as was primarily recorded in catchments where individual household furnaces were found. Both mild and intense rainfalls intensified the surface run-off, which contributed to soil erosion, causing the transport of both Hg and Hg to the river bed. However, the soil was more enriched with labile mercury in anthropogenic catchments, as they are only slightly overgrown with vegetation, the presence of which limits soil erosion. During periods of snow melting, there was intensive leaching and transportation of Hg, which had been deposited on the land surface during the intensive combustion of fossil fuels. In each of the designated periods, stable mercury sulphide was formed in the soil. However, the highest proportion of HgS was found during a period of drought, when organic matter decomposed and there was inflow of sulphur compounds from farms. Taking into consideration the anomalous study periods, the largest load of mercury introduced along with the bed sediment of the Gizdepka into the sea was recorded during downpour/flood. Nevertheless, the most bioavailable Hg-enriched load was introduced during snow melting period.