A fisheries research cruise conducted in 2000 offered a first opportunity to take simultaneous measurements of the activities of three enzymes in mesozooplankton samples collected at a regional scale over the continental shelf of the Bay of Biscay in the NE Atlantic, with the aim of characterizing main aspects of the functioning of the biotic environment of small pelagic fish populations. The activity of the digestive endopeptidase trypsin was selected to characterize the assimilation rate of proteins, whereas pyruvate kinase (PK) was chosen as an indicator of carbohydrate assimilation and aspartate transcarbamylase (ATC) provided an overall assessment of mesozooplankton productivity. The Bay of Biscay region is subject to various strong physical driving forces that directly affect the primary structure of the pelagic food web. On our cruise, the phytoplankton biomass distribution reflected these different physical influences: diatoms dominated the nutrient-enriched coastal water; picoplankton dominated the northern-centra I part where nutrients were depleted; and nanoplankton were abundant at the shelf break where internal waves provided an input of nutrients. These and other results (on bacteria, particulate organic carbon distribution, among others) illustrate the differences that exist in the microbial food webs of different sectors of the bay. The living matter produced was characterized by the quality and quantity of the smallest prey items that were available to higher trophic levels. Variations in mesozooplankton enzyme activities may agree well not only with classically expected results, but also present unexpected special features: high ATC specific activities were measured around the mouth of the Gironde, in the nutrient-rich desalted water of the plume, but surprisingly not in front of the Loire river. PK specific activities reflected preponderantly the balance between phytoplankton cells sizes and the related bacterial abundance resulting from nutrient limitation (mainly P), that induces varying carbohydrates production potential. Trypsin specific activities were moderately variable. except in a restricted area where a highly abundant protein content characterized the particulate matter and in the plume of water flowing out of the Gironde. It is concluded that the presented approach of the metabolism of mesozooplankton communities may provide novel views on crucial processes occurring at the mesoscale, which fits in generally well with the scales of ecological factors mostly influential on small pelagic fish populations. (C) 2009 Elsevier Ltd. All rights reserved.