Summer habitat use by sympatric Arctic charr Salvelinus alpinus, young Atlantic salmon Salmo salar and brown trout Salmo trutta was studied by two methods, direct underwater observation and electrofishing, across a range of habitats in two sub‐arctic rivers. More Arctic charr and fewer Atlantic salmon parr were observed by electrofishing in comparison to direct underwater observation, perhaps suggesting a more cryptic behaviour by Arctic charr. The three species segregated in habitat use. Arctic charr, as found by direct underwater observation, most frequently used slow (mean ±s.d. water velocity 7·2 ± 16·6 cm s−1) or often stillwater and deep habitats (mean ±s.d. depth 170·1 ± 72·1 cm). The most frequently used mesohabitat type was a pool. Young Atlantic salmon favoured the faster flowing areas (mean ±s.d. water velocity 44·0 ± 16·8 cm s−1 and depth 57·1 ± 19·0 cm), while brown trout occupied intermediate habitats (mean ±s.d. water velocity 33·1 ± 18·6 cm s−1 and depth 50·2 ± 18·0 cm). Niche overlap was considerable. The Arctic charr observed were on average larger (total length) than Atlantic salmon and brown trout (mean ±s.d. 21·9 ± 8·0, 10·2 ± 3·1 and 13·4 ± 4·5 cm). Similar habitat segregation between Atlantic salmon and brown trout was found by electrofishing, but more fishes were observed in shallower habitats. Electrofishing suggested that Arctic charr occupied habitats similar to brown trout. These results, however, are biased because electrofishing was inefficient in the slow‐deep habitat favoured by Arctic charr. Habitat use changed between day and night in a similar way for all three species. At night, fishes held positions closer to the bottom than in the day and were more often observed in shallower stream areas mostly with lower water velocities and finer substrata. The observed habitat segregation is probably the result of interference competition, but the influence of innate selective differences needs more study.