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Abstract We measured dissolved organic carbon (DOC) and total dissolved amino acid (TDAA) in seawater and sediment porewater of the Ulleung Basin in the East/Japan Sea. The DOC and TDAA concentrations were 1.1‐ and 1.4‐fold higher in the euphotic zone, and 11‐ and 43‐fold higher in sediment porewater, respectively, than those in the deep ocean. Consequently, in the deep ocean, TDAA and DOC input fluxes from porewater were 2‐ and 0.4‐fold of those from the euphotic zone, respectively. This larger contribution of benthic flux for TDAA and its shorter residence time in the benthic boundary layer (BBL) (1.3 ± 0.9 yr) seem to result in steep TDAA increases in the BBL, although DOC concentrations remained relatively uniform throughout the entire deep ocean. AA‐derived indices also show enhanced bioavailability of dissolved organic matter in the BBL. Benthic inputs seem to supply a significant amount of bioavailable TDAA to the deep ocean, fueling microbial activity.