The size and structure of an animal’s brain is typically assumed to result from either natural or artificial selection pressures over generations. However , because a fish’ s brain grows continuously throughout life, it may be particularly responsive to the environmental conditions the fish experiences during development. Salmon are an ideal model system for studying these effects because natural habitats differ significantly from the hatchery environments in which these fish are frequently reared. For example, in the wild, salmon alevins (i.e. yolk-sac fry) are buried in the gravel, while hatchery environments lack this structural component. We show that the simple manipulation of adding stones to a standard rearing tank can dramatically alter the growth of specific brain structures in steelhead salmon alevins (Oncorhynchus mykiss). We found that alevins reared with stones grew brains with significantly larger cerebella than genetically similar fish reared in conventional tanks. This shift to a larger cerebellar size was, in turn, accompanied by changes in locomotory behaviors – behaviors that correlate strongly to the function of this brain region. We next show that hatchery fish reared in a more naturalistic setting in the wild had significantly larger brains than their lab-reared counterparts. However, relative cerebellar volumes were similar between wild-reared alevins and those reared in the complex treatment in the laboratory. Together our results indicate that, within the first three weeks of life, variation in rearing environment can result in brain differences that are commonly attributed to generations of selection. These results highlight the need to consider enrichment strategies when designing captive rearing facilities for both conservation and laboratory use.