Coupled plankton/small pelagic (SP) fish systems were analysed to assess how foodweb structure influences the export of carbon to pelagic fish during the spring bloom in the Bay of Biscay. The investigation of carbon export flows through inverse analysis was supplemented by estimating the carrying capacity for pelagic fish production by applying linear programming. A planktonic foodweb dominated by microbial pathways had the highest trophic efficiency owing to the tight coupling between planktonic trophic levels and predation pressure on mesozooplankton by fish. Moreover, the magnitude of the gap between carrying capacity and estimated carbon export was related to the size structure of primary producers, with the picophytoplankton-based foodweb having the smallest gap and the microphytoplankton-based one the largest gap. Planktonic foodwebs dominated by small autotrophic cells channelled most of their available carbon to pelagic fish production, whereas foodwebs dominated by large phytoplankton were better suited to benthic communities with a large loss of carbon through sedimentation. Although the total carbon available to higher trophic levels does not vary with the size of the main primary producers, the potential export to SP fish depends on the structure of the planktonic foodweb.