© Inter-Research 2016. Shelf waters of the Cantabrian Sea (southern Bay of Biscay) are productive ecosystems with a marked seasonality. We present the results from 1 yr of monthly monitoring of the phytoplankton community together with an intensive sampling carried out in 2 contrasting scenarios during the summer and autumn in a mid-shelf area. Stratification was apparent on the shelf in summer, while the water column was comparatively well mixed in autumn. The size structure of the photoautotrophic community, from pico-to micro-phytoplankton, was tightly coupled with the meteo-climatic and hydrographical conditions. Over the short term, variations in the size structure and chlorophyll content of phytoplankton cells were related to changes in the physico-chemical environment, through changes in the availability of nutrients and light. Uncoupling between the dynamics of carbon biomass and chlorophyll resulted in chlorophyll to carbon ratios dependent on body size. The slope of the size dependence of chlorophyll content increased with increasing irradiance, reflecting different photoacclimation plasticity from pico-to micro-phytoplankton. The results have important implications for the productivity and the fate of biogenic carbon in this region, since the size dependence of photosynthetic rates is directly related to the size scaling of chlorophyll content.