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Abstract Paleotemperature histories derived from lake sediment archives provide valuable context for modern and future climate changes. Branched glycerol dialkyl glycerol tetraether (brGDGT) lipids are a valuable tool in such pursuits due to their empirical correlation with temperature and near ubiquity in nature. However, the relative contributions of terrestrial and lacustrine sources of brGDGTs to lake sediments is site‐dependent and difficult to constrain. Here, we explored the potential for intact brGDGTs—the complete lipids with polar head groups (HGs) still attached—to provide insight into the sources of brGDGTs on the landscape and their contributions to the sedimentary record in a set of Arctic lakes. We measured core and intact brGDGTs in soils, surface and downcore sediments, water filtrates, and sediment traps across five lake catchments in the Eastern Canadian Arctic, with an emphasis on Lake Qaupat (QPT), Baffin Island. Soils were dominated by brGDGTs with a monoglycosyl (1G) HG, while lacustrine samples contained more phosphohexose (PH) brGDGTs, providing evidence for in situ brGDGT production in both settings. Core‐ and PH‐brGDGT‐IIIa were more abundant in sediments than in the soils or water column, implying an additional post‐depositional source of brGDGTs. A hierarchical clustering analysis indicated that core brGDGTs in Lake QPT sediments were largely lacustrine in origin, while 1G‐brGDGTs were primarily soil‐derived. Additionally, we found evidence for preservation of intact brGDGTs—especially 1G‐brGDGTs—downcore on thousand‐year timespans, though in situ production deeper in the sediment column cannot be ruled out. Finally, we explored the possibility of reconstructing 1G‐brGDGT‐derived soil temperatures and core‐brGDGT‐derived lake temperatures in tandem from sedimentary archives.