Carbon cycling in natural ecosystems is a biologically mediated process with global consequences. Recent work has revealed the important role that lakes play in the global carbon cycle, suggesting organic carbon burial in small lakes and reservoirs matching and even surpassing that of the world's oceans. While much is known regarding biogeochemical cycling of carbon in the water column and underlying sediments of freshwater and marine systems, less is known about permanently redox-stratified water bodies. The modern ocean is fully oxygenated, however, the ocean is thought to have been redox-stratified throughout much of Earth's history, and seasonal redox-stratification is an increasing problem in many freshwater systems due to eutrophication driven by human land usage and warming resulting from global climate change. To better understand carbon signals preserved in the rock record from times of ocean redox-stratification as well as the effects of increasing redox-stratification on carbon cycling in modern freshwater systems, we have characterized the concentration and stable isotopic signal of inorganic and organic carbon in permanently redox-stratified Fayetteville Green Lake (FGL), New York. The results of these analyses indicate that: (1) groundwater is the primary source of dissolved inorganic carbon (DIC) at FGL; (2) organic carbon is extensively cycled within the water column and upper sediments resulting in an increasingly isotopically depleted DIC pool; (3) cyanobacteria-driven carbonate precipitation in the oxic zone is the primary source of carbonate in the sediments; (4) methane concentrations increase below the chemocline with extremely negative δ13C values (−99.1‰ to −102.3‰).