Dissolved organic carbon (DOC) and particulate organic carbon (POC) distribution in the water column were investigated at eight hydrological stations, located in the Ionian Sea, during January 1999. DOC and POC exhibited values in the range 50–73 μM and 0.7–2.7 μM, respectively, in the surface waters, and 31–62 μM and 0.2–0.8 μM in the intermediate and deep waters. The main water masses circulating in the Ionian were identified through potential temperature (θ) versus salinity (S) diagrams and their distribution patterns were verified in the cross-basin longitudinal sections of temperature and salinity. In particular, the water masses formed in the Cretan Sea (southern Aegean), specifically the Cretan Intermediate Water (CIW) and the Cretan Deep Water (CDW), outflowing through the Cretan straits, occupy similar deep horizons as the Levantine Intermediate Water (LIW) and Eastern Mediterranean Deep Water (EMDW) of Adriatic origin, respectively. DOC exhibited different concentrations in each water mass; its range was 39–42 μM in the LIW, 54–62 μM in the CIW, 31–36 μM in the EMDW of Adriatic origin, 43–47 μM in the CDW, and 44–48 μM in the EMDW of the western-central Ionian. The highest DOC concentrations were found in the water masses originated in the Aegean Sea and in the EMDW of the western-central Ionian. Further, DOC versus apparent oxygen utilization (AOU) relationships were investigated within each water mass. In both intermediate and deep waters the results showed linear correlations between DOC and AOU, although with a different sign and slope.