Small pelagic fish represent an essential link between lower and upper trophic levels in marine pelagic ecosystems and often support important fisheries. In the Bay of Biscay in the north-east Atlantic, no obvious controlling factors have yet been described that explain observed fluctuations in European sardine Sardina pilchardus and European anchovy Engraulis encrasicolus stocks, in contrast to other systems. The aim of this study was therefore to investigate to which extent these fluctuations could be trophodynamically mediated. The trophic ecology of both fish species was characterised over three contrasting periods (spring 2010 and 2011 and autumn 2011) in the area, in relation to potential variation in the abundance and composition of the mesozooplankton resource. Stable isotope analyses of carbon (δ13C) and nitrogen (δ15N) were performed on potential mesozoplanktonic prey items and in the muscle of adult fish, as well as in the liver whenever available, and mixing models were applied. In both springs, the mesozooplankton resource was abundant but qualitatively different. During this period of the year, results based on muscle isotope values in particular showed that S. pilchardus and E. encrasicolus likely do not compete strongly for food. On the medium term, E. encrasicolus always presented a greater trophic plasticity than S. pilchardus, both in terms of feeding areas and in the size of the mesozooplanktonic prey consumed. In autumn, mesozooplankton abundances were lower, and it was likely that S. pilchardus and E. encrasicolus share food resources during this period. No clear links between the variation in the mesozooplanktonic resource and the trophic segregation maintained between adults of both fish species in spring could be made. Although a certain potential exists for trophodynamically mediated fluctuations of both species under specific abiotic conditions (i.e. due to the existing trophic segregation in spring in particular), the overall results suggest that fluctuations in abundance of both fish species are probably not directly linked to their trophic ecology in the Bay of Biscay, at least at the level of adult individuals.