We examined the total diatom flux and species composition, total coccolith flux and total mass flux collected with a sediment trap between October 1993 and January 2006 in the northeastern entrance of the Gulf of Lions (North Western Mediterranean). The average daily diatom and coccolith fluxes (3 × 107 valves m2 d–1 and 6.1 × 108 coccoliths m2 day−1, respectively) are comparable in magnitude with previously reported data sets in other high productivity areas of the Western Mediterranean. The temporal particle flux pattern reflected the variations in surface oceanographic conditions and primary productivity, which showed strong annual cycling. Highest diatom, coccolith and total mass fluxes always occurred during the winter–spring transition, while minima were observed during summer. Changes in the diverse diatom communities reflected the water column conditions throughout the record. The intensity of the diatom winter–spring blooms seemed to be enhanced in those years with intense and cold winds during winter, whereas years with low winter wind stress were liable to be less productive for diatoms. Coccolith fluxes exhibited a more stable interannual pattern than diatom fluxes. Significant discrepancies were found between the sediment trap and surficial sediment diatom assemblages.