Global environmental change alters the production, terrestrial export, and photodegradation of organic carbon in northern lakes. Sedimentary biogeochemical records can provide a unique means to understand the nature of these changes over long time scales, where observational data fall short. We deployed in situ experiments on two shallow subarctic lakes with contrasting light regimes; a clear tundra lake and a dark woodland lake, to first investigate the photochemical transformation of carbon and nitrogen elemental (C/N ratio) and isotope (δ13C, δ15N) composition in lake water particulate organic matter (POM) for downcore inferences. We then explored elemental, isotopic, and spectral (inferred lake water total organic carbon [TOC] and sediment chlorophyll a [CHLa]) fingerprints in the lake sediments to trace changes in aquatic production, terrestrial inputs and photodegradation before and after profound human impacts on the global carbon cycle prompted by industrialization. POM pool in both lakes displayed tentative evidence of UV photoreactivity, reflected as increasing δ13C and decreasing C/N values. Through time, the tundra lake sediments traced subtle shifts in primary production, while the woodland lake carried signals of changing terrestrial contributions, indicating shifts in terrestrial carbon export but possibly also photodegradation rates. Under global human impact, both lakes irrespective of their distinct carbon regimes displayed evidence of increased productivity but no conspicuous signs of increased terrestrial influence. Overall, sediment biogeochemistry can integrate a wealth of information on carbon regulation in northern lakes, while our results also point to the importance of considering the entire spectrum of photobiogeochemical fingerprints in sedimentary studies.