•Controls on GDGT distributions in Arctic lakes are studied.•GDGTs are ubiquitous in Arctic lakes.•Strong correlation between branched GDGTs and warm season temperature.•Correlations are consistent with bGDGT–temperature relationships in the tropics.•Data suggest bGDGTs are produced mostly in summer. Understanding the causes and potential ecological and environmental impacts of recent and future temperature changes in the Arctic requires a better understanding of long term climate variability. Amongst the most promising new geochemical tools for sedimentary paleotemperature reconstructions are those based on the glycerol diakyl glycerol tetraethers (GDGTs). Although a number of studies have recently developed empirical calibrations for the temperature sensitivity of isoprenoid GDGTs (i.e., the TEX86 index) and the branched GDGTs (i.e., the MBT/CBT index) in mid and low latitude lakes, there is very little data from lakes in the Arctic. Here, we examine the temperature and environmental controls on GDGT abundances in a transect of small lakes (n=59) distributed across Baffin Island in the eastern Canadian Arctic. Isoprenoid and branched GDGTs are ubiquitous in these lakes. The temperature control on the isoprenoid GDGT distributions is weak, although there is a significant relationship between the branched GDGT distributions and warm season temperature. Furthermore, published relationships developed between branched GDGTs and mean annual air temperatures in tropical lakes yield reconstructed temperatures from Arctic lakes that are consistent with Arctic summer air temperature. This suggests that empirical calibrations from branched GDGTs in lakes reflect the seasonality of branched GDGT production. For example, at low latitudes there is little seasonality in temperature, and branched GDGT production records air temperatures throughout the year. In the Arctic however, branched GDGTs are likely produced in summer, when the temperatures are warmest, sunlight hours are greatest and ice cover is diminished. Due to the extreme seasonality and short window of Arctic productivity, the use of branched GDGTs for summer paleotemperature reconstructions likely remains robust back through time. However, interpretations of paleotemperatures from branched GDGTs in temperate lakes may require careful consideration about potential changes in the seasonal timing of branched GDGT production.