Ten reaches of an Atlantic stream located in north-west Spain were sampled intensively during one summer to characterize the conditions where Atlantic salmon Salmo salar have been re-introduced along the stream. Fish species richness and diversity showed a downstream increase, which was mainly attributed to the higher number of cyprinid species found in the lower reaches. Moreover, except for brown trout Salmo trutta that appeared to be the most ubiquitous species, the densities of the other species was higher in the lower than in the upper stream reaches. Redundancy analysis showed that the pattern of fish assemblages observed along the studied stream was mainly related to the expected gradient observed in the levels of dissolved oxygen, discharge and mean current speed. There was a significant differentiation between midstream and downstream reaches, both in terms of the composition of their fish assemblages and the freshwater habitat. This study emphasizes the importance of describing the variations in fish assemblages and habitat characteristics along a river to explore its relation to potential changes in the survival of fish populations. In particular, the development of habitat–fish relationships may be a useful tool for water managers to assess the effects of development and restoration projects on the habitat of S. salar.