Seasonal dietary shifts by Arctic charr (Salvelinus alpinus (L.)) are common in subarctic lakes, but less is known about how the shift to pelagic zooplankton feeding during the growing season affects stable isotope ratios and mercury concentrations. We sampled Arctic charr, zooplankton and benthic macroinvertebrates from oligotrophic Lake Galggojavri, northern Norway, in June, August and September. Stomach content, age, total length, weight, condition and sex were recorded for all individuals, and liver and muscle tissues were sampled for stable isotope (δ¹³C, δ¹⁵N) and total mercury analyses. We predicted that a dietary shift to zooplankton would lead to depleted ¹³C and increased mercury levels in charr. Arctic charr consumed benthic prey in June, but shifted to zooplankton feeding in August–September. Stable isotope mixing models revealed increased pelagic reliance towards September. Mercury content in liver increased from June to September, whereas muscle showed opposite trend. In stepwise multiple regression analyses, mercury content in muscle was explained by fish length, month and δ¹³C (R ² = 0.46), whereas in liver month, δ¹³C and δ¹⁵N were the main explaining factors (R ² = 0.69). Seasonal dietary shifts appeared to have an effect on total mercury content in charr, and thus sampling month should be considered when designing future monitoring programmes.