As remnants of living organisms, alkenones and isoprenoid glycerol dialkyl glycerol tetraether lipids (isoGDGTs) are widely used biomarkers for determining ocean water temperatures from the past. The organisms that these proxy carriers stem from are influenced by a number of environmental parameters, such as water depth, nutrient availability, light conditions, or seasonality, which all may significantly bias the calibration to ambient water temperatures. Reliable temperature determinations thus remain challenging, especially in higher latitudes and for undersampled regions. We analyzed 33 sediment surface samples from the southern Chilean continental margin and the Drake Passage for alkenones and isoGDGTs and compared the results with gridded instrumental reference data from the World Ocean Atlas 2005 (WOA05) and previously published data from an extended study area covering the central and western South Pacific towards the Aotearoa / New Zealand continental margin. We show that for alkenone-derived sea surface temperatures (SSTs), the widely used global core-top calibration of Müller et al. (1998) yields the smallest deviation of the WOA05-based SSTs. On the contrary, the calibration of Sikes et al. (1997), determined for higher latitudes and summer SSTs, overestimates modern WOA05-based SSTs in both the annual mean and summer. Our alkenone SSTs show a slight seasonal shift of ∼ 1 °C at the southern Chilean margin and up to ∼ 2 °C in the Drake Passage towards austral summer SSTs. Samples in the central South Pacific, on the other hand, reflect an annual mean signal. We show that for isoGDGT-based temperatures, the subsurface calibration of Kim et al. (2012a) best reflects temperatures from the WOA05 in areas north of the Subantarctic Front (SAF). Temperatures south of the SAF are, in contrast, significantly overestimated by up to 14 °C, irrespective of the applied calibration. In addition, we used the GDGT [2]/[3] ratios, which give an indication of the production depth of the isoGDGTs and/or potential influences from land. Our samples reflect a subsurface (0-200 m water depth) rather than a surface (0-50 m water depth) signal in the entire study area and show a correlation with the monthly dust distribution in the South Pacific, indicating terrigenous influences. The overestimation of isoGDGT surface and subsurface temperatures south of the SAF highlights the need for a reassessment of existing calibrations in the polar Southern Ocean. Therefore, we suggest a modified Southern Ocean tetraether index (TEX86)-based calibration for surface and subsurface temperatures, which shows a lower temperature sensitivity and yields principally lower absolute temperatures, which align more closely with WOA05-derived values and also OH-isoGDGT-derived temperatures.