A coastal station located in the southern Bay of Biscay was sampled on six occasions between 12 July and 10 September 1991. The vertical distribution of the patterns of photosynthetic carbon incorporation into proteins, polysaccharides, lipids and low molecular weight metabolites, as well as the biochemical composition of particulate matter were determined on each cruise. In addition, the same variables were monitored during microcosm experiments in which sub-surface phytoplankton assemblages were incubated under different rates of increasing irradiance simulating differences in upwelling intensity. During the first three experiments, phytoplankton cells did not show any growth response to the simulated upwelling conditions. When phytoplankton growth was slow or absent and nutrients were still available, the relative synthesis of proteins was high, suggesting that phytoplankton cells tended to maintain the synthesis of proteins rather than storage products under adverse growth-limiting conditions. Sub-surface phytoplankton assemblages had the potential for growth in response to upwelling. Several diatom blooms developed during the last two experiments showing enhanced levels of protein and polysaccharide specific synthesis rates (SSR) and a marked increase in the protein to carbohydrate (P:C) compositional ratio. Parallel sea-truth observations carried out during an upwelling pulse indicated that phytoplankton assemblages under natural conditions underwent similar physiological changes to those found in the experimental microcosms under simulated upwelling. In general, the most remarkable increases in chlorophyll a (Chl a) concentration and macromolecular SSR took place in those microcosms showing higher rates of increasing irradiance. Variations in the patterns of photosynthate partitioning and the P:C ratio were also related to the intensity of the advective process. These results emphasize the importance of the fine variability of the physical held in modulating the physiological responses of phytoplankton to upwelling.