The concentrations of suspended particulate pigments, C37-C38 alkenones, total organic carbon and nitrogen in the Ligurian Sea (northwestern Mediterranean) have been studied at 5 and 30 m depth during well defined thermocline conditions. An accurate description of the short term changes of these compounds has been achieved by means of four 36-h sampling cycles each encompassing consecutive filtration periods of 4 h. During sampling the thermocline changes were followed closely by simultaneous measurements of water column temperature, salinity and other physical parameters. The analysis of the collected samples indicates that the Haptophyte pigments and alkenones are essentially synthesized at the levels of highest primary production and therefore the C37 alkenone record reflects the seawater temperature at this depth level. The study also shows that part of these alkenones are distributed throughout the water column in association to the suspended particles. This process results in C37 alkenone distributions that, due to their high resistance to chemical and microbial degradation, record the temperature of the highest primary productivity layers even at shallow (e.g., 5 m depth) or deep (e.g., 1100 m depth) waters.