To determine where and when glycerol dialkyl glycerol tetraether (GDGT) membrane lipids in lakes are produced, we collected descending particles in Lake Lucerne (Switzerland) using two sediment traps (at 42 and 72 m water depth) with a monthly resolution from January 2008 to late March 2009. Suspended particulate matter (SPM) was monthly filtered from the water column at three different depths. The potential application of GDGTs in palaeoenvironmental and palaeoclimatic reconstructions was investigated by comparing core lipids and their relative GDGT distribution, with lake water temperatures throughout the year. Fluxes of GDGTs and their concentrations in the water column vary according to a seasonal pattern, showing a similar trend in the SPM and sediment traps. Fluxes and concentrations of isoprenoid GDGTs increase with depth, maximum values being observed in the deeper part of the water column, indicating production of isoprenoid GDGTs by Thaumarchaeota in the deep (similar to 50 m), aphotic zone of Lake Lucerne. The flux-weighted averages of the proxies TEX(86) (0.27) and BIT (0.03) based on the total extracted GDGTs are similar at both trap depths. A sediment core from the same location showed that in the first few centimetres of the core TEX(86) and BIT values of 0.29 and 0.07, respectively, are similar to those recorded for descending particles and SPM, indicating that the sedimentary TEX(86) records the annual mean temperature of deeper waters in Lake Lucerne. TEX(86) values are slightly higher below 20 cm in the core. This offset is interpreted to be caused by the present-day trophic state of the lake, which probably resulted in a deeper niche of the Thaumarchaeota. Branched GDGTs represent only a minor fraction of the total GDGTs in the lake and their origin remains unclear. Our data reveal that GDGTs in lakes have a large potential for palaeoclimatic studies but indicate that knowledge of the system is important for accurate interpretation.