We have determined stable carbon isotope ratios of epifaunal and shallow infaunal benthic foraminifera in the Mediterranean Sea to relate the inferred gradient of pore water δ 13 C DIC to varying trophic conditions. This is a prerequisite for developing this difference into a potential transfer function for organic matter flux rates. The data set is based on samples retrieved from a well-defined bathymetric range (400–1500 m water depth) of sub-basins in the western, central, and eastern Mediterranean Sea. Regional contrasts in organic matter fluxes and associated δ 13 C DIC of pore water are recorded by the δ 13 C difference (Δ δ 13 C Umed-Epi ) between the shallow infaunal Uvigerina mediterranea and epifaunal species ( Planulina ariminensis , Cibicidoides pachydermus, Cibicides lobatulus ). Within epifaunal taxa, the highest δ 13 C values are recorded for P. ariminensis , providing the best indicator for bottom water δ 13 C DIC . In contrast, C. pachydermus reveals minor pore water effects at the more eutrophic sites. Because of ontogenetic trends in the δ 13 C signal of U. mediterranea of up to 1.04 ‰, only tests larger than 600 µm were used for the development of the transfer function. The recorded differences in the δ 13 C values of U. mediterranea and epifaunal taxa (Δ δ 13 C Umed-Epi ) range from −0.46 to −2.13 ‰, with generally higher offsets at more eutrophic sites. The measured δ 13 C differences are related to site-specific differences in microhabitat, depth of the principal sedimentary redox boundary, and TOC content of the ambient sediment. The Δ δ 13 C Umed-Epi values reveal a consistent relation to C org fluxes estimated from satellite-derived surface water primary production in open-marine settings of the Alboran Sea, Mallorca Channel, Strait of Sicily, and southern Aegean Sea. In contrast, Δ δ 13 C Umed-Epi values in areas affected by intense resuspension and riverine organic matter sources of the northern to central Aegean Sea and the canyon systems of the Gulf of Lion suggest higher C org fluxes compared to the values based on recent primary production. Taking regional biases and uncertainties into account, we establish a first Δ δ 13 C Umed-Epi -based transfer function for C org fluxes for the Mediterranean Sea.