This study examines the magnitude and seasonal patterns of dissolved N export during the 2006 melt season from two small watersheds on Melville Island, in the Canadian High Arctic. The dominant N species was dissolved organic nitrogen (DON), comprising >80% of the seasonal nitrogen flux from both rivers. The total DON and dissolved inorganic nitrogen (DIN, NH4++NO3) yields from the catchments were similar (183 and 204 kg DON, and 46–42 kg DIN): however, on a per unit area basis the West catchment had greater yields of both DON and DIN. There were also differences in the temporal patterns and concentrations of the N species between the catchments, which may be a function of inter-catchment differences in vegetation cover. Low end-of-season DIN concentrations in the West river suggest there is strong biogeochemical retention of inorganic N in this catchment during the growing season relative to the East catchment, where stream NO3 concentrations increase through July. A decrease in DOC:DON ratios in the East river at the end of season also indicates a change in the composition of dissolved organic matter in this river that is not evident in the West river. The results illustrate that there can be large differences in the processes controlling nitrogen between two adjacent and similar catchments.