With a view to conducting a comprehensive assessment of pollution of the water bodies within the Lake Baikal drainage basin using dimensionless indicators of the water chemical composition, the problems of identifying and testing the indicators were dealt with, which are necessary for determining the sources and levels of pollution and assessing the contributions of the tributaries to lake pollution and the self-cleaning ability of the waters. The methodology of geoecological monitoring as suggested by these authors is based on identifying correlations between polluters and environmental sites by examining technogenic material of from the sites as mixtures, and material from the sources as their components. Identification of the spatio-temporal structure of pollution involves analyzing the landscape organization of the lake drainage basin and the distribution patterns of pollutants. Substantiation of the observation and monitoring network, extrapolation of monitoring results and display of real-time data used landscape mapping methods. An analysis was made of the landscape and geochemical differentiation of the Lake Baikal drainage basin, and the unified indicators of water composition relating water pollution to natural conditions were ranked. The study revealed areas of geosystems with different rates of organic matter decomposition, i.e. the water areas of the lake with a different self-cleaning ability of the waters, and the areas of the drainage basin, the soils of which are responsible for the formation of waters of different types. The resulting contours were generalized in accordance with the scale of the map for the spatial differentiation of biogeochemical parameters of the landscape organization of the drainage basin. The highest decomposition rate of organic matter is characteristic for taiga dark-coniferous geosystems of optimal development, submontane and intermontane depressions and valleys of Khamar-Daban Range, and the lowest rate is typical for goletz and subgoletz geosystems as well as for taiga forests along the western coast of Lake Baikal.Keywords: Baikal, basin, geoecological monitoring, pollutants, sources of pollution, method of mixing, decomposition rate of organic matter.