High biota mercury levels are persisting in the Arctic, threatening ecosystem and human health. The Arctic Ocean receives large pulsed mercury inputs from rivers and the atmosphere. Yet the fate of those inputs and possible seasonal variability of mercury in the Arctic Ocean remain uncertain. Until now, seawater observations were possible only during summer and fall. Here we report polar night mercury seawater observations on a gradient from the shelf into the Arctic Ocean. We observed lower and less variable total mercury concentrations during the polar night (winter, 0.46 ± 0.07 pmol l−1) compared with summer (0.63 ± 0.19 pmol l−1) and no substantial changes in methylmercury concentrations (summer, 0.11 ± 0.03 pmol l−1 and winter, 0.12 ± 0.04 pmol l−1). Seasonal changes were estimated by calculating the difference in the integrated mercury pools. We estimate losses of inorganic mercury of 208 ± 41 pmol m−2 d−1 on the shelf driven by seasonal particle scavenging. Persistent methylmercury concentrations (−1 ± 16 pmol m−2 d−1) are probably driven by a lower affinity for particles and the presence of gaseous species. Our results update the current understanding of Arctic mercury cycling and require budgets and models to be reevaluated with a seasonal aspect.