The recent increase in temperature and freshwater runoff in the Arctic will influence the functioning of the plankton ecosystem and hence the life of the fish larvae residing in these areas. Here, we studied the strength of physical–biological linkages and the adaptability of individual larval fish species to changing hydrographical and feeding environments in a sub-Arctic area in Greenland. The study was carried out along a transect covering a wide range of physical conditions from the deep ocean to the icecap in the Godthåbsfjord on the south-western Greenland coast. Along the transect, we identified a series of distinct zooplankton and larval fish assemblages which showed linkage to water mass characteristics, to the presence of frontal structures and to availability of preferred prey. Spawning site location and water circulation was also likely to influence distributional patterns of the individual larval fish species. Larvae were feeding on a variety of prey taxa and sizes; some larval species were generalists, while others were more specialized or fed on alternative prey taxa. Differences in feeding strategies might have the consequence that the species will be differently affected by changes in the plankton community. Accordingly, fish larvae that have a greater feeding flexibility and that are more adaptable to environmental variability may cope better with climate related changes.