Observations over the last 20 yr of the development of pelagic and benthic communities of a western European coastal ecosystem (Bay of Brest) provide complementary hypotheses to the 'silicic acid pump' hypothesis. An increase in nitrogen inputs, independent of silicic acid levels, has lowered the Si:N molar ratios during the last 20 yr in river discharges. Since 1981, maximum concentrations of chlorophyll a during the first spring bloom of the annual cycle have decreased, in contrast to the subsequent spring and summer blooms. Concomitantly, extensive spreading of an exotic gastropod Crepidula fornicata has modified the trophic structure of benthic communities by increasing suspension-feeder biomass. The following hypotheses on ecosystem functioning are made: (1) the decrease of chlorophyll biomass during the first spring bloom results from silicic acid limitation and increased suspension feeder activity, (2) benthic filtration and biodeposition activities enhance biogenic silica retention at the sediment-water interface, and (3) recycling of trapped biogenic silica maintains diatom populations by providing silicic acid in summer and reduces primary production seasonality. These hypotheses suggest that benthic organisms control the export rate of biogenic silica towards the open-water ocean and thus the specific composition of secondary phytoplankton blooms in the Bay.