The trade-off between cognitive capacity and developmental costs drive brain size and morphology across fish species, but this pattern is less explored at intraspecific level. Physical habitat complexity has been proposed as a selection pressure on cognitive capacity that shapes brain morphology of fishes, but development of brain is also inherently linked to supply of energy and nutrients, particularly of omega-3 long-chain polyunsaturated fatty acids (n-3 LC-PUFA). In this study, we compared brain morphology of brown trout Salmo trutta from stream, lake, and hatchery environments, which differ in physical complexity and availably of dietary n-3 LC-PUFA ranging from low habitat complexity and high n-3 LC-PUFA availability in hatchery to high habitat complexity and low n-3 LC-PUFA availability in streams. We found that brain size, and size of optic tectum and telencephalon differed across the three habitats, being largest in lake fish. We suggest that these differences appeared to associate with diet quality and habitat specific behavioural adaptations rather than physical habitat complexity.