Thaumarchaeota are one of the most abundant groups of Archaea in the marine water column. Their membrane consists of isoprenoid glycerol dibiphytanyl glycerol tetraethers (GDGTs) which are applied in the widely used TEX86 proxy to reconstruct past sea surface temperatures (SSTs). However, in some specific marine systems, such as the Mediterranean Sea, core-top TEX86-derived temperatures do not seem to reflect annual mean SSTs. This has been attributed to contributions of deep-water dwelling Thaumarchaeota. Here, we investigate the potential causes of this bias by studying both the archaeal diversity as well as the intact polar lipid (IPL) GDGT composition in the Mediterranean water column by a combined 16S rRNA gene amplicon sequencing and a lipidomic approach on suspended particulate matter (SPM) at different water depths. The archaeal distribution showed a dominance of archaea other than Thaumarchaeota, i.e. Marine Euryarchaeota group II and III in the upper epipelagic waters (0-100 meters deep), while Thaumarchaeota (Marine group I; MGI) dominated the subsurface and the deeper waters. This shift in the archaeal community composition coincided with a decrease in IPL GDGT-0 and increase of IPL crenarchaeol. The ratio of GDGT-2/GDGT-3 increased with water depth, but values were lower than observed in deep marine waters of some other regions. The increase of the GDGT-2/GDGT-3 ratio coincided with the high relative abundance of deep-water MGI, which may be linked to the high temperature and salinity found in specific water masses of the Mediterranean Sea. We conclude that these particularities of the Mediterranean Sea are responsible for the overestimated SST based on TEX86.