Biological concentrations of methylmercury(MeHg) are elevated throughout the Arctic Ocean; however, to date, the major sources and the spatial variability of MeHg are not well quantified. To identify the major inputs and outputs of MeHg to the Arctic shelf water column, we measured MeHg concentrations in the seawater and sediment samples from the East Siberian Sea collected from August to September 2018. We found that the MeHg concentrations in seawater and pore water were higher on the slope than on the shelf, while the MeHg concentrations in the sediment were higher on the shelf than on the slope. We created a mass budget for MeHg and found that the benthic diffusion and resuspension largely exceed other sources, such as atmospheric deposition and river water input. The major sinks of MeHg in the water column were dark demethylation and evasion. When we extrapolated our findings on benthic diffusion to the entire Arctic shelf system, the annual MeHg diffusion from the shelf sediments was estimated to be 23,065 ± 939 mol yr⁻¹, about 2 times higher than previously proposed river discharges. Our study suggests that the MeHg input from shelf sediments in the Arctic Ocean is significant and has been previously underestimated.