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The paper presents the results of complex geoecological, hydrochemical and water-ecological studies of the mouth area of tributaries and shores of Lake Baikal at model sites. The mouth area of tributaries is in dynamic interaction with the receiving water body; chemical and biological accumulative and exchange processes directly affect the state of the Lake Baikal’s water resources. The study assessed the transformation and determined potential resilience of the main components of landscapes to anthropogenic loads within the mouth area. Revealed are the basic parameters of soil and surface water pollution and factors of anthropogenic influence of residential and recreational zones on the natural complexes of the model territories. The research results showed that the pollutant accumulation on the geochemical barriers of soils and alluvial deposits, purification of surface waters in floodplain meadow and wetlands are quite active and generally support the ecological state of the mouth area. However, the low degree of resilience to anthropogenic loads and the current level of degradation of the landscape components of mouth complexes indicate the need to reduce the adverse impact on these territories and on the lake ecosystem as a whole.