Based on a multidisciplinary survey in the Iberian upwelling during late summer 2007, this paper analysed comparatively the cross-shore variability and offshore transport across the upwelling front and within a mesoscale filament. Along the East-West (EW) sections, transient upwelling pulses bring regularly cold, fresh and nutrient-enriched waters to the surface, triggering intense biological responses. Offshore advection by wind-forced Ekman drift of the successive fronts, interrupted by relaxation periods, drive the variability of the planktonic communities. While the near-shore areas are dominated by relatively small phytoplankton controlled by mesozooplankton grazing, large cells of diatoms appear after a short decay. Although microphytoplankton dominates largely the shelf communities, the species composition varies during the offshore drift with the apparition of dinoflagellates and the gradual development of large zooplankton individuals. The oligotrophic ecosystem characterised by small organisms and low biomass (similar to 80 km offshore) contrasts strongly with the transitional area and the coastal upwelling. The low density waters within the filament and the existence of a pair of opposite rotating eddies at its base and tip promote its generation and rapid seaward extension. The intensified offshore advection of coastal enriched waters considerably increases the area favouring a productive ecosystem (until similar to 160 km off the coast). Cross-shelf variability of bio-physical variables is observed in the filament as along EW sections, although a subsequent homogenisation within the mesoscale structure erases the sharp fronts. Off the shelf within the filament, the chlorophyll a is distinctly organised as a shallow subsurface maximum dominated by nano-phytoplankton. The relative physical isolation of a dynamical food-web in the filament is also promoting nutrient remineralisation under the structure. Finally, we estimate that mesoscale filaments, although being less extended meridionally than the upwelling front itself (similar to 40% of the length of the front) are responsible for a greater offshore transport of chlorophyll (similar to 60% of total cross-shelf exchanges) over the Iberian system. Despite the favourable wind pulses advecting westward the successive upwelling fronts, self-propelled filaments provide permanent offshore transport, even under wind relaxation period, thus playing a major role in cross-shelf exchanges. (C) 2013 Elsevier Ltd. All rights reserved.