This paper performs a detailed study of a wide set of organic-geochemical proxies in 15 sediment cores collected from the main basins of Lake Baikal (the northern, the central and the southern) where processes of focused fluid discharge were detected. A variety of studied zones in-cludes sites with gas and hydrothermal seepage, mud volcanoes with or without gas-oil fluid dis-charge, gas hydrates and authigenic carbonates. The composition of the dispersed organic matter and individual hydrocarbon molecular markers (n-alkanes, dimethyl alkanes, isoprenoids, steranes, terpanes and polycyclic aromatic hydrocarbons) testify to the input from predominantly allochtho-nous terrestrial and autochthonous microbial and algal sources. The studied sources, maturity and biodegradation parameters of organic matter vary significantly for areas with different fluid dis-charge. The composition of specific biomarkers including isoprenoids and immature hopanoids re-flects the lateral and vertical changes of microbial activity in sediments associated with various environmental conditions. The identified types of terpanes distribution (mature, mixed and imma-ture) correlate well with types of fluid discharge and attest to the development of various methano-genic and methanotrophic microbial communities in sediments. Moreover, the revealed specificity of microbial molecular markers distribution allowed us to suggest the fluid discharge processes in zones where they were not previously detected.