A total of 337 samples collected from five sediment traps located in the Gulf of Lions, Catalan margin and the Alboran Sea have been analyzed in order to study the seasonal, interannual and geographical distributions of silicoflagellate fluxes in the Western Mediterranean. As a general trend, maximum fluxes of silicoflagellate skeletons always occurred during the spring bloom; i.e. during the winter–spring transition, while minimum fluxes were recorded during summer, characterised by a strong stratification and oligotrophic conditions. However, the sediment trap record of the Catalan margin did not exhibit any clear seasonal signal, probably owing to the fertilizing effect of the rivers Llobregat and Besos. Regarding interannual variability, no clear relationship between the NAO (North Atlantic Oscillation) and the silicoflagellate fluxes was found. In contrast, the silicoflagellate assemblages from the Alboran Sea and the Gulf of Lions responded with low fluxes and a delay in their annual maximum to the anomalous conditions elicited by the 1997–98 El Niño Event. Furthermore, the 2003 summer heat wave over the Western Mediterranean had similar repercussions on the silicoflagellate spring maximum 2004 in the Gulf of Lions. Three silicoflagellate species were identified in the samples, following the taxonomic concepts of Throndsen (1997): Dictyocha fibula (Ehrenberg), Dictyocha speculum (Ehrenberg) and Octactis octonaria (Ehrenberg) Hovasse 1946. D. fibula was cosmopolitan and the dominant species at all sites, always accounting for more than 80%. Moreover, its maximum fluxes were recorded in those sampling sites which were under the influence of high nutrient concentrations caused by the river input. D. speculum was only recorded in the northern locations, which suggests an affinity for colder water masses. In contrast, O. octonaria was restricted to the Alboran Sea stations, where temperatures reached the highest values and nutrients were scarcer.