We assessed the food resource partitioning of three fish species (Arctic charr, Atlantic salmon and alpine bullhead) living in sympatry in a subarctic river. Fish were sampled monthly during the ice-free season (May–October), and dietary overlap among the species was calculated according to Schoener’s index. In October, the diet overlap among all three species was high (>70%). In contrast, large to modest food resource partitioning occurred among Arctic charr and the other two species from May to September (27–59% overlap), whereas there was a distinct diet overlap between Atlantic salmon and alpine bullhead in May, August and September (>64%), but not in July (53%). Surface prey (terrestrial and emerged aquatic insects), probably caught at the surface, were important for Arctic charr in August and September (24.9 and 46.6%, respectively), whereas the other fish species mainly fed on Apatania stigmatella, Mystrophora intermedia and Ephemerella aurivilli. Alpine bullhead seemed to feed close to the bottom, Atlantic salmon used both the bottom and water of various depths, whereas Arctic charr showed the greatest capacity to forage at the water surface. This vertical segregation may be important for fish assemblages in subarctic rivers, allowing food resource partitioning and coexistence of sympatric species.