The initial focus of the PELGAS integrated survey was to assess the small pelagic fish biomass in the Bay of Biscay in springtime, for fisheries management purposes. Sampling has been extended to produce long-term time-series of spatially-explicit data and indices, describing the main pelagic ecosystem components: hydrology, phytoplankton, mesozooplankton, fish and megafauna. A collaborative analysis of these datasets has brought new insights on the Bay of Biscay pelagic ecosystem summarized here. New results on single ecosystem components include an analysis of water samples to groundtruth the results of an ocean color algorithm aiming at detecting phytoplanktonic coccolithophores. New insights on mesozooplankton spatio-temporal distribution and energy content have been derived from the analysis of net samples. Adult anchovy and sardine energy content have been studied along a latitudinal gradient, and across different age stages. Changing patterns in the relative abundance of marine megafauna have been evidenced at a community level. Cross-ecosystem component studies are also presented. Actual dates of the annual survey have been corrected, with respect to a surface temperature climatology, allowing for an improved interpretation of anchovy and sardine spawning. Spring habitats of small pelagic fish communities in the Bay of Biscay have been characterised. Fluctuations in habitat preferences of five mobile top predators species have been assessed. Predation of cetaceans on small pelagic fish has been investigated, based on stomach contents. The spatial structure of the ecosystem has been characterised, to map consistent ecosystem seascapes and study their variability in time. Dominant ecological processes in the Bay of Biscay have been identified based on series of potential pelagic ecosystem indicators derived from the survey, and the effects of external forcing on the ecosystem dynamics tested. Perspectives for the survey are discussed in the context of the European Marine Strategy Framework Directive and the Common Fisheries Policy.