<p>Threespine stickleback (<i>Gasterosteus aculeatus</i>) are known for their rapid adaptation to a wide range of environments. However, despite having served as a model species for ecology, evolution, and developmental biology, little is known about the ontological dietary changes of juvenile individuals in the wild. This has created a gap in our knowledge, given that the organismal phenotype is largely moulded during the juvenile phase, and natural selection during this life stage is often strong. Lake Mývatn, Iceland, offers a unique setting to explore these early-life organism-environment interactions due to its high habitat and resource heterogeneity, as well as divergent adult stickleback feeding morphologies across habitats. Here, we tested whether diet, based on gut content analysis, and trophic morphology have diverged between juveniles from different habitats and if diet composition covaries with morphology and body size. Overall, we saw clear differences in diet composition among distinct habitats within the lake, and morphological divergence in head morphology (e.g. gape size) among contrasting habitats. Juveniles tended to either have many small Cladocera or Chironomidae larvae in their diet; smaller individuals tended to have more Cladocera, and bigger individuals consumed more Chironomidae larvae. Such an ontogenetic diet shift is congruent with laboratory and other field studies on juvenile stickleback. However, this is one of the first studies, to investigate the association between juvenile diet and head morphology in wild freshwater stickleback. Thus, the study delivers unique insight into the development of trophic morphology, as well as diet-mediated diversification in threespine stickleback. </p>