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The present study describes the fluxes and transports of nutrients and chlorophyll a inferred from direct observations carried out off south Portugal, during a research cruise in early October 2006. The covered area corresponds to the western part of the northern margin of the Gulf of Cadiz, from Cape São Vicente (9.0°W) till the Guadiana River mouth (7.4°W). Unlike in the western Iberian margin, the upwelling in this region is rather intermittent during the summer season. It is interleaved by periods when warm waters coming from the eastern part of the Gulf of Cadiz occupy the coastal region. However, our observations were taken during an intense upwelling event that took place at the end of the upwelling season. Ten meridional transects were sampled in a total of 90 CTD casts. Current velocity profiles were acquired along the ship's track with a hull-mounted acoustic Doppler current profiler (ADCP). The analysis of the circulation field and water masses characteristics led to the quantification of the fluxes and transports of chlorophyll a and nutrients in 5 meridional transects along the coast. Results show the prevalence of the alongshore eastward flow over the offshore Ekman transport in the coastal circulation without formation of upwelling filaments. Transport of chlorophyll a showed a near surface maximum (<30dbar), while transport of nutrients were generally higher in the layer below (30–100dbar). The estimates show net eastward alongshore transports of chlorophyll a and nutrients into the Gulf of Cadiz and weak cross-shore exchanges. At the deepest levels, the estimates of the transports by the shallow vein of the Mediterranean Water show an important input of nutrients to the Atlantic. However, waters in the top 100dbar, impoverished in nutrients by biological utilisation due to upwelling, show that nitrate and phosphate transports provided into the Gulf of Cadiz exceed those carried westward by the shallow vein of the Mediterranean Water. [ABSTRACT FROM AUTHOR]