Results of study of pore waters of bottom sediments from different Baikal basins are presented. The most typical ion distribution patterns reflecting the Baikal sediment diagenesis are given. We have established that in areas with regular sedimentation, in the absence of faults and inflows, the sediment pore waters of three lake basins inherit the chemical composition of the Baikal water, which is stable in time and space. Changes in pore water composition mark general natural anomalies, such as the presence of active faults, tectonic movements, and inflows along permeable zones. In areas with the subsurface occurrence of gas hydrates, thorough long-term research has revealed an anomalous composition of pore waters. It has been established that the anomalies are caused by a discharge of deep-level mud-volcanic fluids. The ejected mud-volcanic waters differ from each other in mineralization, ion composition, and sources, which determines the difference in hydrate formation and the composition of gas hydrates.