Small pelagic fish have shown a general decrease in size and body condition over the past two decades in several European regional seas. Although the underlying processes are still not well understood, recent studies point to a bottom-up control. In order to better understand how the environment impacts the main individual life history traits through phenotypic plasticity, we developed a comparative approach between two species, European anchovy and sardine, and across three regions of the Northeast Atlantic and Mediterranean Sea, namely the English Channel, the Bay of Biscay and the Gulf of Lion. We developed a bioenergetic modeling framework based on Dynamic Energy Budget theory (DEB). The first part of this work focuses on testing the bottom-up hypothesis at the individual scale. While this mechanistic framework successfully reproduced the spatial differences in size across the three studied regions, the temporal trends in the environment (temperature and zooplankton) were not strong enough to explain the drastic decrease in size through time. Through a scenario approach, we estimated the decrease in zooplankton quantity or quality required to reproduce the decrease in small pelagic size. Secondly, we assessed the effect of this bottom-up control on fish biomass and size distribution by scaling up to the population level using an existing DEB-IBM (Individual Based Model) in the Bay of Biscay. We also assessed the effects of population drivers, e.g. density-dependence, fishing and selective mortality, on population dynamics.