An experiment was performed in four artificial stream channels during summer and autumn to investigate the effects of biotic and abiotic factors on habitat choice of juvenile Atlantic salmon (Salmo salar). To investigate factors determining habitat choice, the stream channels had sloped river beds creating two distinct habitats (shallow and deep). The main factor, large Atlantic salmon present (large present), was the most important factor affecting juvenile habitat choice during summer time experiments. During autumn experiments, the two main factors large Atlantic salmon present and time of day (exclusive for autumn experiments), were important factors affecting habitat choice. The highly significant effect on juvenile habitat choice of having a large Atlantic salmon present identifies inter-cohort competition and/or risk of predation as important factors affecting habitat choice in juveniles. This, in turn, could have direct or indirect effects on juvenile survival and growth. The differences between proportions of fish in the deep between night and day highlights a diel change in habitat use by juveniles.