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Quantitative temperature reconstructions from lacustrine organic geochemical proxies including branched glycerol dialkyl glycerol tetraethers (brGDGTs) and alkenones provide key constraints on past continental climates. However, estimation of air temperatures from proxies can be impacted by non‐stationarity in the relationships between seasonal air and water temperatures, a factor not yet examined in strongly seasonal high‐latitude settings. We pair downcore analyses of brGDGTs and alkenones measured on the same samples through the Holocene with forward‐modeled proxy values based on thermodynamic lake model simulations for a western Greenland lake. The measured brGDGT distributions suggest that stable autochthonous (aquatic) production overpowers allochthonous inputs for most samples, justifying the use of the lake model to interpret temperature‐driven changes. Conventional calibration …