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Changes in structural connectivity as it can affect functional connectivity, the biological and behavioural responses of an organism, has been examined here over 2 contrasting years when the spatial distribution of larval and juvenile cod and their prey shifted from the flank to the crest on Georges Bank. New data on the gut contents of pelagic juvenile cod are compared with known prey distributions, potential growth and how climate warming can change connectivity in this region. Centropages spp. was the most important prey for pelagic juveniles, especially in June 1987 when they had high abundance on the crest and were dominant in the cod stomachs. In June 1986, copepod abundance was low where the juveniles were distributed along the flank. The potential growth of juvenile cod was greater in June 1987, consistent with the higher abundance of Centropages spp., and with higher recruitment survival, compared with June 1986. Annual changes in the spatial distribution of cod early life stages within the environment of cold or warm years can have different impacts on their growth and survival. Whereas the small copepods, Pseudocalanus spp., are primary prey for cod larvae and very abundant in cold years, larger copepods, Calanus finmarchicus and Centropages spp., are important prey for the pelagic juveniles and the latter species can have a high impact in warm years on the crest. The different spatial structure during cold or warm years provides an explanation why different year classes respond differently to environmental change. Depending on the presence or absence of specific prey, the functional connectivity response changes pathways that determine the growth and survival of early life stages and ultimately a role in recruitment.