In the reconstruction of sea surface temperature (SST) from sedimentary archives, secondary sources, lateral transport and selective preservation are considered to be mainly negligible in terms of influencing the primary signal. This is also true for the archaeal glycerol dialkyl glycerol tetraethers (GDGTs) that form the basis for the TEX86 SST proxy. Our samples represent four years variability on a transect off Cape Blanc (NW Africa). We studied the subsurface production, vertical and lateral transport of intact polar lipids and core GDGTs in the water column at high vertical resolution on the basis of suspended particulate matter (SPM) samples from the photic zone, the subsurface oxygen minimum zone (OMZ), nepheloid layers (NL) and the water column between these. Furthermore we compared the water column SPM GDGT composition with that in underlying surface sediments. This is the first study that reports TEX86 values from the precursor intact polar lipids (IPLs) associated with specific head groups (IPL-specific TEX86). We show a clear deviation from the sea surface GDGT composition in the OMZ between 300 and 600m. Since neither lateral transport nor selective degradation provides a satisfactory explanation for the observed TEX-derived temperature profiles, with a bias towards higher temperatures for both core- and IPL-specific TEX86 values, we suggest that subsurface in situ production of archaea with a distinct relationship between lipid biosynthesis and temperature is a responsible mechanism. However, in the NW-African upwelling system the GDGT contribution of the OMZ to the surface sediments did not seem to affect the sedimentary TEX86 as it showed no bias and still reflected the signal of the surface waters between 0 and 60m. © 2014 Elsevier Ltd.