During the NAUTINIL (September-October 2003), MIMES (July 2004), BIONIL (October 2006) and MEDECO2 (November 2007) cruises, coring and submersible dives were realized in the Nile Deep Sea Fan (NDSF) area. Active fluid venting sites were identified by the presence of living benthic organisms and by methane plumes in the bottom waters above the seeping structures. At all sites, hard carbonate crusts cover irregularly the sea floor. The sediments from the venting areas are organic-rich, contain sometimes carbonate concretions and have a strong H2S smell indicative of active sulfate reduction. The mineralogy of carbonate crusts is dominated by aragonite and Mg-calcite; the mineralogy of concretions is more complex, with mixtures of Mg-calcite, dolomite and ankerite. The oxygen and carbon isotopic compositions of the carbonate from crusts and concretions exhibit large variations (-2.8< δ18O ‰ VPDB <+9.5; -42.6< δ13C ‰ VPDB <+22.4). The wide range of δ18O values reflects variable sources of fluids. Most of the authigenic carbonates from the NDSF were precipitated in isotopic equilibrium with the Mediterranean bottom water. The carbonate crusts and concretions from the brine seeps of the north-western NDSF are enriched in 18O indicating that a source of 18O-rich fluids originated from depth. Differently, a few crusts and concretions from the eastern NDSF exhibit relatively low δ18O values, which are due to precipitation at warm temperatures. The very low δ13C values of the diagenetic carbonates indicate that methane and possibly other heavier hydrocarbons were the major source of carbon that was oxidized as bicarbonate mostly through bacterial sulfate reduction coupled with anaerobic methane oxidation within the anoxic sediment. The very positive δ13C values of the diagenetic carbonates from many carbonate concretions are related to the production of 13C-rich CO2 during methanogenesis within the sub-seafloor sediments.