AbstractThe current knowledge about fish biodiversity and species distributions in Arctic freshwater systems is generally limited. This contrasts the clear urgency for more accurate biodiversity data to assess the effects of future ecosystem challenges such as climate change and other anthropogenic effects. Here we compare traditional electrofishing surveys with environmental DNA (eDNA) for monitoring species distribution of Atlantic salmon (Salmo salar) and Arctic char (Salvelinus alpinus) in the West Greenlandic sub‐Arctic river system of Kapisillit, which contains the only known population of Atlantic salmon in Greenland. Overall, electrofishing and eDNA surveys show high compatibility in regard to species detection and quantification, with Arctic char confirming a significant relationship between eDNA concentration and observed fish abundance. Both methods confirm a shift in species occurrence and relative species abundance through the river system. Specifically, salmon is restricted to the lower warmer sections of the river system while Arctic char is found throughout the system but dominates the upper parts. In total, the study supports eDNA as a promising tool for fish community assessment, which may serve a wide array of applications for Arctic freshwater monitoring. These applications include analyzing species occurrence and distribution of native and invasive species, as well as documenting potential shifts in relative species abundance as shown here. Given the ease of sampling and high sensitivity of the method, eDNA provides a powerful cost‐effective approach capable of detecting species in remote areas as well as corroborating fish community monitoring programs. This may especially be valuable for monitoring in the Arctic where logistic complications with sampling and high operational costs so far constrains routine monitoring.