The aim of this study was to assess bioturbation rates in relation to macrozoobenthos and environmental variables in the Svalbard fjords, Barents Sea and Nansen Basin during spring to summer transition. The results showed differences in benthic community structure across sampled area in relation to sediment type and phytopigment content. Fjords, Barents Sea and the shallow parts of Nansen Basin (<400 m) were characterized by high functional groups diversity, and by biodiffusive and non-local rates ranging from 0.05 to 1.75 cm−2 y−1 and from 0.2 to 3.2 y−1, respectively. The deeper parts of Nansen Basin, dominated by conveyors species, showed only non-local transport rates (0.1–1 y−1). Both coefficients intensity varied with benthic biomass. Non-local transport increased with species richness and density and at stations with mud enriched by fresh phytopigments, whereas biodiffusion varied with sediment type and organic matter quantity. This study quantified for the first time the two modes of sediment mixing in the Arctic, each of which being driven by different environmental and biological situations.