Although freshwater lakes, reservoirs, and peatlands have been identified as potential carbon sinks, detailed reconstructions of carbon accumulation in lakes during the Holocene have been rare. In this study, seismic reflection data and sediment cores up to 6 meters in length were collected from two small lakes in Kejimkujik National Park, Nova Scotia, Canada. Seismic reflection methods, coupled with sediment coring, offer an effective tool in evaluating the depositional history of a lake system and sediment distribution. Calibrated with whole-core, physical property measurements, high-resolution seismic reflection profiles enable the quantitative determination of sediment distribution within the lake, including total sediment mass and thickness. Sub-samples down the length of the cores were measured for organic, inorganic, and total carbon concentrations, roughly representing the Holocene. A precise estimate of lake sediment volume, together with sediment chemistry, allows accurate determination of the magnitude of carbon accumulated during specific time periods. Furthermore, through the use of carbon isotopes, the relative significance of autochthonous and allochthonous inputs to the lake system can determined and related to ecosystem processes and climate change.