Long-term quantitative seasonal temperature reconstructions from the Arctic provide necessary context to evaluate long-term climate-cryosphere sensitivity and climate-carbon cycle feedbacks. Here, we analyze two quantitative molecular paleotemperature proxies, glycerol dialkyl glycerol tetraethers (GDGTs) and long-chain alkenones (LCAs), in the sediments of a small lake in the Kangerlussuaq region of western Greenland which span the past c. 9.5 thousand years (ka) following local deglaciation. Branched GDGT (brGDGT)-inferred summer water column temperature anomalies relative to the uppermost sample (representing roughly the last decade) based on the methylation of branched tetraethers (MBT’5Me) decrease through the mid-to-late Holocene from 3.96 to 0.95°C. However, the co-occurrence of high ratios of the isoprenoid GDGTs caldarchaeol to crenarchaeol and distinct brGDGT distributions suggest hypoxic conditions influenced brGDGT production prior to 4.5 ka (thousand years before present), preventing the application of the MBT’5Me paleothermometer in these samples. LCAs, which we do not detect in sediments older than 5.5 ka, record stronger temperature variability than brGDGTs, with spring water temperature anomalies ranging from –2.1°C to +6.4°C. We reconcile changes in the magnitude and seasonality of LCA and brGDGT temperatures using a thermodynamic lake model forced by simulations under modern and perturbed climatologies. Summer water column temperatures, which are indistinguishable from summer surface water temperatures, and likely recorded by brGDGTs, increase linearly with summer air temperatures. In contrast, surface water temperatures in the two weeks following ice-out, when haptophyte algae bloom and synthesize LCAs, demonstrate substantially stronger interannual variability. However, multi-decadal mean surface water temperatures following ice-out increase linearly with temperature forcing, suggesting LCA-inferred spring water temperatures are biased towards specific years with favorable conditions for haptophyte communities.