In spring 2000, IFREMER organised its yearly fisheries acoustic survey on board R/V 'Thalassa' over the French shelf of Biscay as a multi-disciplinary platform for estimating and mapping the fish and monitoring the pelagic ecosystem. Acoustics and CUFES (continuous underway fish egg sampler) were coupled allowing combined mapping of the adult fish and its spawned eggs. Four major compartments of the plankton ecosystem were extensively sampled on a grid of stations. More than 50 variables were measured in the plankton relating biomass as well as turn over in four compartments, hydrology, nutrients and particulate matter, bacteria and phytoplankton, meso-zooplankton. First, a joint analysis was performed using Multiple Factorial Analysis (MFA). The method allowed for the estimation of a common factorial space in which to represent the structure in each compartment as well as the common structure to all compartments. The most structuring variables were evidenced. Stations were then grouped based on their positions in the common factorial space. The groups were represented spatially and a strong spatial pattern evidenced. Groups were interpreted as functional pelagic entities as they corresponded to different ecosystems at different state in their seasonal evolution. The distribution of the fish and their eggs was analysed in relation to the hydro-plankton entities using geostatistical variography. Sardine and anchovy distributed in different entities but similar for each fish species and its eggs. Anchovy was shown to be associated with a lesser number of hydro-plankton entities than sardine. Anchovy was more confined to its entities than sardine which crossed the entity borders. Last, the interest in measuring size fractionated chlorophyll during fisheries surveys in Biscay was discussed as the study showed that this parameter enabled to track the river plume hydro-plankton entity in which anchovy spawned.