Scientific and methodological problems are examined of the pollutant dispersion within inland water bodies and water courses by interaction between the fluxes at the divides of water, atmosphere and near-tobottom areas (Putyrsky, 1993). With the use of a semi-empirical turbulent diffusion equation, regularities in the pollutant area from technogenic sources were investigated with taken into account the sedimentation processes. Mathematical models have been developed for modeling the processes of accumulation of pollutants in the bottom sediments off-shore and water systems in river valleys. Analyzed were also the data on migration of the carcinogenic components within Lake Valday (North-western Russia). A method has been proposed for the quantitative estimation of a number of hydro-physical factors through an approximation of experimental data by any equations theoretically proved as well as mathematical solutions of the inverse problems.