The database presents the field data used within the study carried out in the north-western Adriatic Sea (Brigolin et al., 2018, Biogeosciences https://doi.org/10.5194/bg-2017-206). A longline mussel farm was taken as a local source of perturbation to the natural Particulate Organic Carbon (POC) downward flux. This flux was first quantified by means of a pelagic model of POC deposition coupled to sediment traps data, and its effects on sediment bioirrigation capacity and OM degradation pathways were investigated constraining an early diagenesis model by using original data collected in sediment porewaters. The measurements were performed at stations located inside and outside the area affected by mussel farm deposition.