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Lipid biomarkers preserved in marine sediments provide powerful tools for reconstructing past climate and environmental change. However, their interpretation critically depends on understanding the processes governing their production, transport, and preservation, as different water-column processes can substantially modify the environmental signals transferred to sedimentary archives. This study investigates four different lipid biomarkers (long-chain fatty acids [LCFA], n-alkanes, alkenones, and glycerol dialkyl glycerol tetraethers [GDGTs]) at three key stages of their source-to-sink pathway: production, transport in the water column, and deposition and preservation in surface sediments to shed light on their controlling processes factors. A particular focus is placed on tracking sea surface temperature (SST) signals encoded in some of these lipids at each key stage, thereby refining the current framework for biomarker-based paleotemperature reconstruction in the study region.We collected suspended particulate matter from six southwest Iberian Margin stations (JC089 cruise, August 2013) using in situ filtration pumps yielding 38 samples (~1188 L on average per sample) from surface to ~3000 m depth at discrete fluorescence and turbidity maxima. Surface sediments from the same locations and 25 additional core-top samples were also analyzed. LCFA, n-alkanes, and alkenones were quantified using GC-FID, while GDGTs were analyzed by HPLC. Associated SSTs were reconstructed using the Uk′₃₇ and TEX₈₆ indices, with Bayesian calibrations applied to both proxies.In the water-column, concentrations of terrestrial lipids (n-alkanes and LCFA) are highest in the upper photic zone with no clear onshore–offshore trend, reflecting mixed atmospheric and riverine inputs. Alkenones are predominantly found in nearshore waters within the photic zone and decrease in concentration with distance offshore, reflecting in situ production linked to primary productivity. Elevated GDGT concentrations are found above ~2000 m within the warm, saline, and relatively turbid Mediterranean Outflow Water (MOW). While this distribution suggests some lateral transport, the absence of alkenones at these depths points to substantial in situ GDGT production.Both alkenone (12.6–22.3 °C) and GDGT-derived SSTs (14.6–20.0 °C) exhibit a cold bias relative to surface CTD measurements in the water column. A similar cold bias is observed in surface sediments, where reconstructed SSTs (15.7–19.0 °C for alkenones; 14.6–19.2 °C for GDGTs) are lower than World Ocean Atlas annual mean values. We attribute these differences to variations in production depth and seasonal bias and furthermore rule out a significant influence from terrestrial GDGT input or riverine nutrients.Future application of compound-specific radiocarbon and stable isotope analyses (δ¹³C, δ²H) on alkenones will further strengthen the mechanistic link between modern lipid cycling and paleoenvironmental reconstructions.