The sustainable exploitation of small pelagic fish populations, characterized by short life span and early age at first reproduction, is typically more influenced by the success of annual recruitment rather than by fishing mortality. Recruitment strength, in turn, is related to the high environmental variability characterizing the pelagic fish habitats, able to strongly affect the survival of early stages, from hatching to recruitment. Here, we consider the case study of anchovy (Engraulis encrasicolus) stock in the Strait of Sicily (Central Mediterranean). The interannual fluctuations exhibited over an 18-year long period by this fish population was found to be mainly linked to surface circulation patterns, as far as they are able to control retention/dispersal processes of larval stages. We firstly used Lagrangian simulations to reproduce the fate of anchovy early stages during their planktonic phase. Larval retention indices constructed from the output of the simulations were able alone to explain a large proportion of variance (up to 70%) in yearly biomass of the anchovy population, outclassing the other environmental factors considered in this study. Such results are relevant for fisheries management, for all fish stocks characterized by potentially high vulnerability of early life stages.