The newly introduced temperature proxy, the tetraether index of archaeal lipids with 86 carbon atoms (TEX86), is based on the number of cyclopentane moieties in the glycerol dialkyl glycerol tetraether (GDGT) lipids of marine Crenarchaeota. The composition of sedimentary GDGTs used for TEX86 paleothermometry is thought to reflect sea surface temperature (SST). However, marine Crenarchaeota occur ubiquitously in the world oceans over the entire depth range and not just in surface waters. We analyzed the GDGT distribution in settling particulate organic matter collected in sediment traps from the northeastern Pacific Ocean and the Arabian Sea to investigate the seasonal and spatial distribution of the fluxes of crenarchaeotal GDGTs and the origin of the TEX86 signal transported to the sediment. In both settings the TEX86 measured at all trap deployment depths reflects SST. In the Arabian Sea, analysis of an annual time series showed that the SST estimate based on TEX86 in the shallowest trap at 500 m followed the in situ SST with a 1 to 3 week time delay, likely caused by the relatively low settling speed of sinking particles. This revealed that the GDGT signal that reaches deeper water is derived from the upper water column rather than in situ production of GDGTs. The GDGT temperature signal in deeper traps at 1500 m and 3000 m did not show a seasonal cyclicity observed in the 500 m trap but rather reflected the annual mean SST. This is probably due to a homogenization of the TEX86 SST signal carried by particles as they ultimately reach the interior of the ocean. Our data confirm the use of TEX86 as a temperature proxy of surface ocean waters.