The endorheic Lake Van in eastern Anatolia (Turkey) is the world's largest soda lake and it is an important site in paleoclimate studies to understand past continental conditions in western Asia. In order to gain further insights into the biomarker signatures in Lake Van's sediments we have analyzed particulate material in sediment traps deployed between August 2006 and July 2007. The biomarkers used were long chain alkenones (LCAs C37-C39, haptophyte lipids), isoprenoid glycerol dialkyl glycerol tetraethers (GDGTs, Archaea membrane lipids) and pigments (chlorins and fucoxanthin). The biomarker fluxes indicate a strong seasonality in export primary productivity and the phytoplankton community structure. The highest total mass and organic carbon fluxes were found in summer, coupled to strong stratification while the lowest mass fluxes occurred in winter at the time of water column mixing. With increasing temperatures in early spring, phytoplankton export productivity grew, coupled with an increase of total mass flux and organic carbon, which might be associated to enhanced nutrient input from snowmelt runoff. The percentage of C37:4 shows some correspondence with observed seasonal changes in Lake Van's stratification structure. We also evaluated the potential applicability of molecular temperature proxies derived from Archaea and haptophyte lipids. The use of the TEX86 proxy was precluded by low GDGT abundances. Estimated LCA temperatures were consistent with temperatures in the photic zone but no seasonality changes were observed despite the wide annual temperature range measured at Lake Van. © 2011 Elsevier Ltd.