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This research is aimed at detailed study of deep-water depositional system, recently discovered in Lake Baikal and named the Khuray system. It has been formed in the Quaternary in a narrow rift basin with the concurrent modern tectonic activity and characterised by a unique structure. The main feature is a presence of canyons, not only in proximal but also in a distal part of the system. Transit part is very wide and is characterized by numerous branches and merges of the channels. The analysis of sediments and seismic profiles shows a change in the activity and morphology of the Khuray system over time. Also it allows to reconstruct its development in the late Pleistocene.