Thawing Arctic permafrost is releasing massive amounts of terrestrial mercury (Hg) into the Arctic shelf, which is expected to form a Hg sink in sediments. Here we analyzed the coupling roles of terrestrial input and biological processes in varying mineral/organic matrix-related Hg sequestration and deposition on the East Siberian Arctic shelf (ESAS), using Pearson and partial correlation analysis. Results show that the occurrence of Hg in the Laptev Sea under the Lena River-dominated input exhibits strong correlations with the organic carbon (OC) content and sediment specific surface area. This indicates that the prolonged riverine loading processes facilitate Hg sequestration by organic/mineral matrices and these land-derived mineral-OC-Hg complexes remain stable during cross-shelf transportation. By contrast, the comparative samples with coastal erosion-dominated Hg input in the western East Siberian Sea shows limited Hg complexation, primarily due to the absence of regulation by riverine processes and/or the high sedimentation rates. The correlations between Hg and OC source proxies (δ13C and lignin) indicate that these matrix-free Hg could be more readily sequestrated by the marine OC, which facilitates its deposition via the biological pump. While unexpectedly low Hg abundance in the Chukchi Sea may indicate that the effective biological scavenging of Hg sequestration could be constrained by insufficient terrestrial Hg input. Our findings of the matrix-related Hg sequestration by mineral and/or OC association in this study may shed light on the biogeochemical cycle of Hg in the Arctic aquatic regime, which could reduce the methylmercury formation in water column, and the methylation within sediments needs further exploration.