Changes in concentration and composition of Iatroscan-measured dissolved lipids were examined at a daily to month scale, in relation to the hydrological and biological context at a central site of the Ligurian sea, NW Mediterranean during the PECHE-DYNAPROC 2 experiment (14 September to 17 October 2004). Lipid concentrations (excluding hydrocarbons) (TLd-HC) and TLd-HC to DOC ratios in the 0–1000 m water column, varied from 5.3 to 48.5 μg l−1 and 0.01 to 0.09, respectively. The highest TLd-HC concentration values were found in the 0–50 m surface layer, coinciding with phytoplankton biomass. Significant correlations (p<0.01, n=87) between glycolipids from chloroplast membranes, namely the monogalactosyldiacylglycerols, a major component of dissolved lipids (25.1±10.8% of TLd-HC, n=166), and various phytoplankton pigments (chlorophyll cs-170, violaxanthin, diadinoxanthin, zeaxanthin, and lutein), suggested that picoeucaryote phytoplankton were a major source of dissolved lipids. Lipid metabolites (free fatty acids, alcohols, diacylglycerols and monoacylglycerols), an other important component of TLd-HC (37.6±11.1%, n=166), showed a greater degree of degradation of lipids in this transitional period than previously observed earlier in the year. Zooplankton wax and steryl ester biomarkers (WSE) and triacylglycerols showed a distinct periodicity in the mesopelagic layer throughout the period investigated. Concentrations of WSE (5.5–13.6 μg/l) increased in the 0–150 m surface layer, mid-way through the cruise (4–6 October), before the winter mixing. WSE were observed later and deeper in the mesopelagic layer (6–11 October), accompanied by rebounds in hydrocarbons (6–8 October) and phospholipid concentrations (12 October) in the 400–1000 m depth layer. Zooplankton migration and/or fecal pellet egestion, followed by DOM release from POM, were likely responsible for the appearance of these lipid signatures in the mesopelagic layer. Because we observed these signatures during low wind period only (<15 knots: 28 September–12 October), it may indicate that this organic matter transfer to depth was related to undisturbed trophic web in the water column above. The low salinity water lenses that appeared twice during the cruise in the 40–80 m surface layer had little effect on dissolved lipid concentrations. Lower concentrations in phosphoglycerides and hydrocarbons (HC) than in nearby sea water suggested different microbial assemblages and different level of HC contamination in this low salinity water.