Differences in selective environments can greatly influence the behavioral responses that evolve across populations. Domestication involves the removal of some selection pressures typical of natural populations and the modification or intensification of others, resulting in a variety of behavioral changes. Here, we examined the differences in social behavior in wild and domesticated zebrafish (Danio rerio) as a response to habitat manipulation. As zebrafish have evolved in habitats that undergo drastic seasonal fluctuations in water velocity, vegetation cover, and other environmental parameters, we expect wild zebrafish to be behaviorally more flexible across different habitats than domesticated zebrafish. First, we sampled shoaling and aggressive behavior of wild zebrafish in their natural habitat. In a controlled laboratory conditions, we then measured these behavioral responses in wild-caught and domesticated zebrafish in habitats differing in flow regimes. Both wild and domesticated zebrafish rapidly adjusted their shoaling behavior as a response to the water flow. However domesticated zebrafish were more aggressive and formed less cohesive groups compared to wild zebrafish. These observed differences in behavior indicate the strong influence of physical context on the social behavior of zebrafish. Further investigations on population-level variations in behavioral responses will offer a way to distinguish between phenotypic associations resulting from underlying genetic and physiological differences.