Mercury is one of the priority pollutants of our time, but also a unique element that can form organic and inorganic compounds of various degrees of toxicity. The toxicity of mercury is influenced by the form of metal finding, environmental factors, ways of metal and its compounds entering the organisms of living beings, and concentrations. In this paper, we consider the factors that determine the migration and transformation of mercury in complex hydrochemical areas of rivers-estuaries. The research is based on the results of observations carried out since 2004 at the mouths of the Northern Dvina, Pechora and Kyanda Rivers. The hydrological and hydrochemical conditions of waters and bottom sediments have been analyzed. Various forms of the occurrence and migration of mercury in the waters and bottom sediments of the objects under consideration have been studied. Conclusions about the priority factors that determine the behavior of mercury for each water body and, in general, for the estuarine areas of this natural zone have been drawn.