Total (TOC) and dissolved (DOC) organic carbon vertical profiles were analyzed from 11 stations located in various regions of the Mediterranean Sea, together with the distribution of other physical, chemical and biological parameters. TOC showed the highest concentrations (68–83 μM) above the pycnocline, followed by a marked decrease to values of 45–48 μM at 100–200 m. Below 200 m, values of 40–45 μM were observed. The excess TOC and DOC occurring at each station was calculated by subtracting 48 μM from the observed concentrations. The stock of the excess TOC and DOC increased eastward; while surface DOC mineralization rates decreased from 1.5 μM d−1 to 0.26 μM d−1eastward. The integrated average of the biological parameters in the above-pycnocline layer showed a bacterial production versus particulate primary production (BP/PPP) ratio ranging from 22% in the Ionian Sea (MIO station) to 31% in the Ligurian Sea (Dyfamed station), while bacterial carbon demand versus PPP was higher than 100%, considering a bacterial growth efficiency of both 15% and 30%. The data here reported indicate various scenarios of carbon dynamics. At the stations west of the Sardinian Channel, the microbial loop was very active, and a high flux of carbon to the microbial loop (large bacterial and protist abundance) may be hypothesized, which would result in a low DOC concentration. At the stations east of the Sardinian Channel, no significant longitudinal variation was found in DOC and BP. DOC accumulated at these stations, possibly due to bacteria P-limitation, to DOC chemical composition and/or to the occurrence of different prokaryotic populations with a different ability to consume the available DOC.