Seasonal and ontogenetic shifts in the diet of Arctic charr Salvelinus alpinus were studied in a deep, ultra‐oligotrophic lake in subarctic Finland from both stomach contents and the stable carbon (δ¹³C) and nitrogen (δ¹⁵N) isotope compositions of muscle and liver tissues. Both diet and isotope results indicated that the S. alpinus population relied mainly on littoral benthic energy sources. The strong littoral reliance appeared largely independent of season or fish size, although the data lacked small (total length, L_T, <130 mm) and young (<3 years) S. alpinus. Liver isotope values of intermediate‐sized S. alpinus (200–350 mm), however, suggested exploitation of the increase in the abundance of pelagic zooplankton in the late open‐water season. The results suggest that, in general, a strong littoral reliance of fishes can be a feature in subarctic lakes throughout the year. Due to its faster isotopic turnover rate and thus higher resolution for temporal diet changes, liver could be more commonly used in stable‐isotope studies of fish trophic niche shifts instead of using only the less responsive muscle tissue.