The Adriatic sea is generally viewed as a long bay in the Central Mediterranean, stretching SE to NW for 800 km, from the Strait of Otranto to the Gulf of Venice, with an extremely long, geometrically complex coastline, creating a high diversity of hydrodynamic and sedimentary environments. The seafloor slopes down from the North shallow shelf (mean depth 35 m) through the middle Adriatic depression (250 m depth in the Pomo Pit) to the bathyal reached in the Southern Adriatic pit (1260 m). Typical physiographic and climatic features strongly influence biological productivity. The productivity of the Northern Adriatic is among the highest in the Mediterranean, while it becomes lower in the offshore waters of the Central and Southern subbasins, defining clear oligotrophic and benthic-pelagic coupling gradients from the Northern to the Southern edge of the basin. Assessing the benthic response to particulate fluxes of organic matter from the photic layer was a target of the EU-MATER Project. The applied methodological strategy involved measurements of primary production by 14C in situ incubation technique, of particulate fluxes through the water column by moored sediment traps, of sediment community oxygen consumption (SCOC) by in situ and on-deck incubations, and of carbon burial fluxes at three sites in the Southern Adriatic (A1), the Otranto Strait (O2) and the Ionian sea (I1), along the main pathway of outflowing water masses. In this paper, yearly budget calculations of carbon are presented for stations, selected as being representative of wider areas in the three subbasins, to give a picture of the Adriatic basin as a whole. Data from the Northern basin, obtained by the same methodology, come from previous research programmes carried out in the framework of EU Marine projects (STEP/Adria and MTP 1/Euromarge AS). The carbon fraction reaching the seafloor was quantified as the sum of SCOC and burial fluxes and was compared to 14C primary production measurements in the photic zone. Both primary production estimates and carbon respired in the sediment (SCOC) show a clear depth dependence, with the former ranging between 588 g C m-2 year-1 in the Northern shelf off the Po river delta, and 62 g C m-2 year-1 in the Ionian sea, and the latter between 130 and 2 g C m-2 year-1 at the same sites. Burial efficiencies (the ratios of buried carbon to carbon rain) decrease from 47% to 3%. Sediment organic matter lability was investigated through its composition in terms of proteins, lipids and carbohydrates and the sum of their concentrations as expressed in carbon equivalents (biopolimeric carbon fraction, BPC). Compositional differences are clearly indicated between the Northern and the Middle-South Adriatic subbasins due to mixing with terrestrial carbon in the North and longer residence times in the water column in the Middle-South, with the Pomo Pit representing an accumulating site of refractory organic carbon. From carbon budget calculations for the deep sites, taking into account trap measured fluxes to the sediment, lateral input seems to play a role at the deep sites and especially in the Pomo Pit.