Branched glycerol dialkyl glycerol tetraethers (brGDGTs) are analyzed in different lakes of the Mackenzie (Canadian Arctic) and Kolyma (Siberian Arctic) River basins to evaluate their sources and the implications for brGDGT-based paleothermometry in high-latitude lakes. The comparison of brGDGT distributions and concentrations in the lakes with those in river suspended particulate matter, riverbank sediments, and permafrost material indicates that brGDGTs in Arctic lake sediments have mixed sources. In contrast to global observations, distributional offsets between brGDGTs in Arctic lakes and elsewhere in the catchment are minor, likely due to the extreme seasonality and short window of biological production at high latitudes. Consequently, both soil-and lake-calibrated brGDGT-based temperature proxies return sensible temperature estimates, even though the mean air temperature (MAT) in the Arctic is below the calibration range. The original soil-calibrated MBT-CBT (methylation of branched tetraethers-cyclisation of branched tetraethers) proxy generates MATs similar to those in the studied river basins, whereas using the recently revised MBT'-CBT calibration overestimates MAT. The application of the two global lake calibrations, generating summer air temperatures (SAT) and MAT, respectively, illustrates the influence of seasonality on the production of brGDGTs in lakes, as the latter overestimates actual MAT, whereas the SAT-based lake calibration accounts for this influence and consequently returns more accurate temperatures. Our results in principle support the application of brGDGT-based temperature proxies in high-latitude lakes in order to obtain long-term paleotemperature records for the Arctic, although the calibration and associated transfer function have to be selected with care.