The Arctic is rapidly changing, disrupting biogeochemical cycles and the processing, delivery and sedimentation of carbon (C), in linked terrestrial-aquatic systems. In this investigation, we coupled a hydrogeomorphic assessment of catchment soils, sediments and plants with a recent lake sediment sequence to understand the source and quality of organic carbon present in three Arctic upland lake catchments on Disko Island, located just south of the low-high Arctic transition zone. This varied permafrost landscape has exposed soils with less vegetation cover at higher altitudes, and lakes received varying amounts of glacial meltwater inputs. We provide improved isotope and biomarker source identifications for palaeolimnological studies in high-latitude regions, where terrestrial vegetation is at or close to its northerly and altitudinal range limit. The poorly developed catchment soils lead to lake waters with low dissolved organic carbon (DOC) concentrations ([less than or equal to]1.5 mg L.sup.-1). Sedimentary carbon/nitrogen (C/N) ratios, the C isotope composition of organic matter ([delta].sup.13 C.sub.org) and biomarker ratios (n-alkanes, n-alkanols, n-alkanoic acids and sterols) showed that sedimentary organic matter (OM) in these lakes is mostly derived from aquatic sources (algae and macrophytes). We used a .sup.210 Pb-dated sediment core to determine how carbon cycling in a lake-catchment system (Disko 2) had changed over recent centuries. Recent warming since the end of the Little Ice Age (LIAâ¼1860 CE), which accelerated after ca. 1950, led to melt of glacier ice and permafrost, releasing nutrients and DOC to the lake and stimulating pronounced aquatic algal production, as shown by a 10-fold increase in Î²-carotene, indicative of a major regime shift. We also demonstrate that recent increases in catchment terrestrial vegetation cover contributed to the autochthonous response. Our findings highlight that in Arctic lakes with sparsely developed catchment vegetation and soils, recent Anthropocene warming results in pronounced changes to in-lake C processing and the deposition of more reactive, predominately autochthonous C, when compared with extensively vegetated low-Arctic systems.