As known from inland sedimentary records, boreholes, and geophysical data, the initiation of the Baikal rift basins began as early as the Eocene. Dating of volcanic rocks on the rift shoulders indicates that volcanism started later, in the Early Miocene or probably in the Late Oligocene. Prominent tectonic uplift took place at about 20 Ma, but information (from both sediments and volcanics) on the initial stage of the rifting is scarce and incomplete. A comprehensive record of sedimentation derived from two stacked boreholes drilled at the submerged Akademichesky ridge indicates that the deep freshwater Lake Baikal existed for at least 8.4 Ma, while the exact formation of the lake in its roughly present-day shape and volume is unknown. Four important events of tectonic/environmental changes at about approximately 7, approximately 5, approximately 2.5, and approximately 0.1 Ma are seen in that record. The first event probably corresponds to a stage of rift propagation from the historical center towards the wings of the rift system. Rifting in the Hovsgol area was initiated at about this time. The event of ~5 Ma is a likely candidate for the boundary between slow and fast stages of rifting. It is reflected in a drastic change of sedimentation rate due to isolation of the Akademichesky ridge from the central and northern Lake Baikal basins. The youngest event of 0.1 Ma is reflected by the (87)0Sr/ (86)Sr ratio increase in Lake Baikal waters and probably related to an increasing rate of mountain growth (and hence erosion) resulting from glacial rebounding. The latter is responsible for the reorganization of the outflow pattern with the termination of the paleo-Manzurka outlet and the formation of the Angara outlet. The event of approximately 2.5 Ma is reflected in the decrease of the (87)Sr/(86)Sr and Na/Al ratios in Lake Baikal waters. We suggest that it is associated with a decrease of the dust load due to a reorganization of the atmospheric circulations in Mainland Asia. All these tectonic and climatic events could (and actually did) influence the biota of Lake Baikal. The Hovsgol rift basin was shaped to its recent form between 5.5 and 0.4 Ma. However, freshwater Lake Hovsgol appeared only in the latest pre-Holocene time as a result of meltwater inflow and increase of atmospheric precipitations during the Bølling-Allerød warming. Prior to this, a significantly smaller, saline outflow-free precursor of Lake Hovsgol existed. It explains why two, now connected, lakes of similar water chemistry within similar climatic and tectonic conditions differ so much in their biodiversity.