The objective of our work was to reconstruct transgressive-regressive events in the Northern Caspian Sea during the Khazarian epoch of its Pleistocene history to determine the natural conditions of the development of the basins and to assess their response to climate change. This work is based onstudies of the sedimentary formations of the upper part of the Quaternary sequence in the Northern Caspian Sea. The borehole was drilled in the eastern part of the depression Shirotnaya, the sea depth was 11.9 m, and the depth of drilling was 56.4 m. The core was subjected to lithological, malacological, and palynological analysis. This paper discusses the results related to the interval 56.0–26.6 m. The structure, facies-lithological, and malacological composition of the core capture three transgressive stages of the Caspian, namely the Early Khazarian, Late Khazarian, and Hyrcanian stages, separated by regressive phases. The representative spore-pollen assemblages made it possible to carry out the climatic and stratigraphic subdivision of the studied Khazarian deposits and to suggest a provisional version of the history of climatic and phytocenotic events during the sedimentation period. The results of our studies have introduced new discussion points into the paleogeography of the Northern Caspian Sea.