Widespread ecological reorganizations and increases in organic carbon (OC) in lakes across the Northern Hemisphere have raised concerns about the impact of the ongoing climate warming on aquatic ecosystems and carbon cycling. We employed diverse biogeochemical techniques on a high-resolution sediment record from a subarctic lake in northern Finland (70°N) to examine the direction, magnitude and mechanism of change in aquatic carbon pools prior to and under the anthropogenic warming. Coupled variation in the elemental and isotopic composition of the sediment and a proxy-based summer air temperature reconstruction tracked changes in aquatic production, depicting a decline during a cool climate interval between ~1700-1900 C.E. and a subsequent increase over the 20th century. OC accumulation rates displayed similar coeval variation with temperature, mirroring both changes in aquatic production and terrestrial carbon export. Increase in sediment organic content over the 20th century together with high inferred aquatic UV exposure imply that the 20th century increase in OC accumulation is primarily connected to elevated lake production rather than terrestrial inputs. The changes in the supply of autochthonous energy sources were further reflected higher up the benthic food web, as evidenced by biotic stable isotopic fingerprints.