To understand the processes controlling the formation of the sediment record, seasonal variations of living communities, fluxes through the water column, and sediment accumulation rates of diatoms, coccolithophores (phytoplankton), and planktic foraminifera (zooplankton) were studied through seasonal water-column sampling, sediment traps, and box- and multi-core sediment sampling in the Canary Islands region (29°N), from the productive NW African coastal area to offshore oligotrophic waters. A close relationship between the phytoplankton composition and hydrographic conditions was observed. Coccolithophores dominate the phytoplankton community throughout the year. The seasonal flux variability of the various groups as measured in the upper-trap samples (≈500–900 m water depth) reflects the seasonal changes of their vertically integrated standing stocks in the overlying water column. Distinct high-standing stocks of all three groups can be related to the influence of upwelling filaments at the near-shore site (EBC). At the offshore sites (ESTOC and LaPalma) all groups display a late winter/early spring maxima related to local increased production. In addition, the increase in flux of all the organisms observed in the deeper traps at both offshore sites can be explained by lateral advection of living material by surface filaments. In addition, the occurrence in the traps of diatom and foraminifera species characteristic of high-productivity coastal areas indicates that the material must come from a highly productive coastal region, rather than production in the overlying oligotrophic surface water. Investigation of the phytoplankton assemblages in the water column, sediment traps, and surface sediments reveals: (i) sediment assemblages have been somewhat modified both by differential dissolution in the water column and the sediments and possibly also by reworking and (ii) the original composition is fundamentally preserved. Diatoms, in spite of being the most affected by differential dissolution both during settling and within the sediments, show a clear relation to the upwelling process. Planktic foraminifera (zooplankton) appear to be less altered by dissolution. For both groups, however, the dominant taxa during the upwelling episodic events (Chaetoceros and Globigerina bulloides) dominate the assemblages found in the sediments underlying Cape Ghir, the most productive area of the Canary Islands region.