In many exploited marine fish species, older individuals within cohorts often have slower growth rates at age than their younger counterparts, a process generally attributed to fishing. However, environmental changes might also contribute to the selective disappearance of faster growing individuals because of the increasing constraints acting on growth in suboptimal environments. Using otoliths of anchovy and sardine collected each year in spring since 2000 in the Bay of Biscay, we measured individuals’ growth during age-0 and catch-up growth during age-1, and followed their changes in time from 2000 to 2018 to quantify the magnitude of selective mortality. We then determined whether the variations in growth and selective mortality were related to seasonal temperature, food quantity, stock biomass or stock harvest rate. In both species, there was a decline in growth during age 0 over time and a catch-up growth declined in anchovy. Density-dependence had a strong effect on growth in anchovy. In both species, there was a systematic selective disappearance of individuals with large growth at age-0 within each cohort and selection has changed over time to favour individuals with large catch-up growth in anchovy. Moreover, diversifying selection occurred for growth at age-0 in both species and catch-up growth in anchovy. In anchovy, years with high selective disappearance of large individuals, high catch-up growth and high diversifying selection were those in which the harvest rates were high (environmental variables having more limited effect). In sardine, the selective disappearance of large individuals was stronger in years with low food quantity and the magnitude of selection acting on growth was unrelated to this stock’s harvest rate. Though fishing exerted strong selection pressure in anchovy, selective mortality against large growth still occurred even at low harvest rates in both species, suggesting that this might be a natural process affecting these small pelagic forage fish species. Although anchovy and sardine have a similar trophic position, their selection regimes differed due to differences in their stock dynamics, environmental sensitivity, and fishing rate. It might therefore be hazardous to extrapolate the responses of single species to environmental and anthropogenic factors onto others.