In the 2000 and 2001 springtime periods, mesozooplankton samples were systematically taken during research cruises devoted to the study of the distribution and abundance of small pelagic fishes in the French part of the Bay of Biscay, NE Atlantic, continental shelf. Simultaneous activities of three enzymes were measured in these mesozooplankton samples, to characterize the main features of ecosystem function at a regional scale. The aim was to assess assimilation rates of carbohydrates, through pyruvate kinase activity, and protein, through trypsin activity, by the mesozooplankton community and the resulting overall productivity, through aspartate transcarbamylase activity. The highest influence on the pelagic environment was the strong difference in the freshwater outflow rates from the two main large rivers, the Loire and the Gironde, which was principally responsible for the inter-annual fluctuations of the nutrients in the Bay. This overall influence of river flow results in a characteristic pattern of sea-surface salinity, which was reflected by the phytoplankton biomass distribution. Mesozooplankton enzyme activities showed high variations between the two years. The contrast in the dynamics of the pelagic food web processes between the two consecutive years, with higher activity in 2001, affected the nutritional condition of the zooplanktivorous breeding anchovy Engraulis encrasicolus.