As anthropogenic impacts to both climate and freshwater resources continue to intensify in coming decades, an increasing number of lakes will experience carbon cycle perturbations. An examination of lakes that have experienced such perturbations for millennia can clarify the nature and severity of carbon cycle disturbances. Lakes precipitating carbonate minerals provide an opportunity to use measurements of both inorganic and organic carbon isotopes to detect the relationship between the inorganic and organic carbon cycles. We examine these dynamics among three lakes in Yunnan, China, which have been impacted by human activities for the last 1,500 years. We compare the period impacted by people to drying conditions and lowering lake levels during the middle Holocene, and more stable hydrologic conditions during the later Holocene, both of which are characterized by minimal anthropogenic influence. From 5,500 to 3,500 years BP, decreased precipitation, increased evaporation, and changes in vegetation drove increases in sediment carbon isotope values. Despite continued weakening of the Indian monsoon from 3,500 to 1,500 years BP, carbon isotopes values stabilized. Following anthropogenic manipulation of lake levels after 1,500 years BP, and despite differences in the magnitude of activities in the three catchments, a decrease in inorganic carbon isotopes without a parallel change in organic carbon isotopes is a pervasive feature in each system and a clear signature of human activity. We suggest possible drivers are an influx of dissolved inorganic carbon from either oxidized organic matter or dissolved carbonates from the watershed and/or the respiration of lake sediment organic matter.