The history of lacustrine sedimentation in the Sevan depression is traced. The potential of using lacustrine sediments for the analysis of paleoclimate and neotectonic development of the region is shown. The long-term preservation of the lacustrine regime in the Sevan depression is mainly due to large lava flows that repeatedly create dams in the northwestern part of the depression. A coupled analysis of three dated sections of sediments near the coast of Lake Sevan (Dzknaget, Norashen, and Argichi) shows that the main factor determining the lake level fluctuations in the Holocene is the climate: the alternation of eras with varying moisture amounts. Transgression periods are characterized by the accumulation of shallow–lake and beach facies and regression periods are characterized by alluvial and subaerial technogenic (cultural layers) facies. Holocene sediments of Lake Sevan contain synchronous transgressions of the Subarctic, Atlantic and Sub-Atlantic periods and regressions of the Boreal and Subboreal periods. The transgression periods are associated with climate moistening and the development of tree–shrub vegetation in its watershed area, and the regressions correspond to epochs of a decrease in humidity and a reduction of this type of vegetation. The minimum lacustrine sedimentation rates are typical for beach facies that are remote from river mouths (0.1–0.3 mm/year), and the maximum values are typical for delta facies (0.7–1.5 mm/year). The results can be used to analyze and forecast long-term trends in the development of the natural environment in the watershed area of Lake Sevan and changes in its level.