The Arctic, one of the most sensitive components of the Earth's climate system, experienced pronounced climatic fluctuations during the Late Holocene. In order to obtain a detailed record of past environmental and climatic variability, sedimentary cores from two interconnected infilled depositional basins in the Kobbefjord area, southwestern Greenland, were retrieved and subjected to a multi‐proxy investigation. The absolute chronostratigraphy was established through radiocarbon (14C) and short‐lived radioisotope (210Pb, 137Cs) dating. We also analysed magnetic susceptibility, grain size, X‐ray fluorescence element composition, total content of carbon, nitrogen and sulphur, biogenic silica and diatom assemblages. The palaeoenvironmental reconstruction presented from the upper basin records ~800 years of sedimentation in a former shallow Arctic lake/pond that was modulated by catchment processes and regional hydroclimate. The record is dominated by alternating periods of increased organic and clastic deposition, suggesting warmer/drier and colder/wetter climate, respectively. Comparison of our records with other proxy‐based lacustrine, marine and glacier records and instrumental measurements from Greenland and the North Atlantic reveals common climatic trends, consistent with the inferred North Atlantic Oscillation pattern. Periods at ~800–600, ~320–220 and ~140–30 cal. a BP correspond to the main cold phases. The earliest climatic deterioration coincides with the demise of the nearby Norse Western Settlement. The most recent cold period represents the culmination of the Little Ice Age with the maximum Holocene advances of Greenland glaciers. Ameliorated conditions predominated at ~550–320 and ~220–140 cal. a BP. The evolution of both water bodies is concluded by transition into oligotrophic peat bogs after complete infilling of the basins at ~30 cal. a BP. Despite differences in proxy signals between the coring sites, this study endorses the usefulness of shallow lake/pond sediments from infilled basins for environmental reconstructions, as long as local depositional processes do not mask the external driving factors.