One of the causes of climate warming observed in recent decades is the increase in the concentration of greenhouse gases in the atmosphere, where the leading role is played by CO2, through which carbon is transferred between different reservoirs of the planet (lithosphere, biosphere, atmosphere, hydrosphere). Terrestrial aquatic ecosystems are simultaneously receivers, converters, accumulators and exporters of terrigenous and atmospheric carbon. It is possible to estimate the accumulating capacity of a lake in relation to carbon and its changes at different stages of the water body ecosystem development on the basis of the study of bottom sediment cores. The article presents the results of a study of bottom sediments of Lake Chudesnaya Lamba (Kivach Nature Reserve) and reveals the specific patterns of total organic carbon accumulation. Based on the lithological, grain-size and geochemical composition of samples, three horizons were distinguished in the sediment profile, illustrating the successive change of the sedimentation environment in the lake’s evolution, which occurred during climate change and accumulation of mineralogenic, organo-mineralogenic and organogenic sedimentary matter. Horizon I (7.50–7.33 m) is represented by sediments of mineral nature accumulated during the Onego Ice Lake period. Horizon II (7.33–7.26 m) is sediments formed during the period of climate changes after the separation of the lake from the Onego Ice Lake, which are characterized by a significant gradient of organic matter concentrations. Horizon III (7.26–7.10 m) was formed in the Holocene, at which time the reservoir became an accumulator of organic matter. The new information on the content and specific features of organic matter accumulation in Lake Chudesnaya Lamba sediments, along with the use of the balance model of organic matter fluxes in trophic networks, will make it possible to calculate the carbon balance in the ecosystem of the model lake and to produce predictive estimates of CO2 fluxes from the water surface depending on the chemical composition of water and the geographical location of the lake.