An increase in habitat complexity is thought to decrease visibility and the territory size of visually oriented animals. Hence, the addition of physical structure has been viewed as a useful restoration technique to increase the density of territorial species, particularly in stream fishes. However, a decrease in territory size may have a negative effect on the fitness of individual organisms. We attempted to quantify some of the positive and negative effects of increasing habitat structure on the behaviour and growth rate of wild young‐of‐the‐year (YOY) Atlantic salmon. Fish were exposed to one of two habitat treatments in mesh enclosures in Catamaran Brook, New Brunswick: a gravel substrate (low complexity) or a gravel substrate with boulders added (high complexity). Wild‐caught individuals were tagged, weighed and measured before being stocked at densities of 1·m⁻² for 7‐d trials. While fish from high‐complexity treatments benefited from lower rates of aggression, they also had lower foraging rates and smaller territories compared to those in low‐complexity treatments. Specific growth rate, however, did not differ significantly between treatments. While the addition of structure to a habitat may be beneficial at the population level in terms of an increase in population density, our results suggested that individual fish may pay some short‐term costs in these environments. Further research is needed to evaluate the longer term costs and benefits of adding structure to improve the habitat quality for stream salmonids.