Climate change driven increases in permafrost thaw and terrestrial runoff are expected to facilitate the mobilization and transport of mercury (Hg) from catchment soils to coastal areas in the Arctic, potentially increasing Hg exposure of marine food webs. The main aim of this study was to determine the impacts of seasonal riverine inputs on land-ocean Hg transport, zooplankton diet and Hg bioaccumulation in an Arctic estuary (Adventfjorden, Svalbard). The Adventelva River was a source of dissolved and particulate Hg to Adventfjorden, especially in June and July during the river's main discharge period. Stable isotope and fatty acid analyses suggest that zooplankton diet varied seasonally with diatoms dominating during the spring phytoplankton bloom in May and with increasing contributions of dinoflagellates in the summer months. In addition, there was evidence of increased terrestrial carbon utilization by zooplankton in June and July, when terrestrial particles contributed substantially to the particulate organic matter pool. Total (TotHg) and methyl Hg (MeHg) concentrations in zooplankton increased from April to August related to increased exposure to riverine inputs, and to shifts in zooplankton diet and community structure. Longer and warmer summer seasons will probably increase riverine runoff and thus Hg exposure to Arctic zooplankton.