In Mediterranean seas and coastal zones, rivers can be the main source of mercury (Hg). Catchment management therefore affects the load of Hg reaching the sea with surface runoff. The major freshwater inflows to the Baltic Sea consist of large rivers. However, their systems are complex and identification of factors affecting the outflow of Hg from its catchments is difficult. For this reason, a study into the impact of watershed land use and season on mercury biogeochemistry and transport in rivers was performed along two small rivers which may be considered typical of the southern Baltic region. Neither of these rivers are currently impacted by industrial effluents, thus allowing assessment of the influence of catchment terrain and season on Hg geochemistry. The study was performed between June 2008 and May 2009 at 13 sampling points situated at different terrain types within the catchments (forest, wetland, agriculture and urban). Hg analyses were conducted by CVAFS. Arable land erosion was found to be an important source of Hg to the aquatic system, similar to urban areas. Furthermore, inflows of untreated storm water discharge resulted in a fivefold increase of Hg concentration in the rivers. The highest Hg concentration in the urban runoff was observed with the greatest amount of precipitation during summer. Moderate rainfalls enhance the inflow of bioavailable dissolved mercury into water bodies. Despite the lack of industrial effluents entering the rivers directly, the sub-catchments with anthropogenic land use were important sources of Hg in the rivers. This was caused by elution of metal, deposited in soils over the past decades, into the rivers. The obtained results are especially important in the light of recent environmental conscience regulations, enforcing the decrease of pollution by Baltic countries.