Four mud volcanoes of several kilometres diameter named Amon, Osiris, Isis, and North Alex and located above gas chimneys on the Central Nile Deep Sea Fan, were investigated for the first time with the submersible Nautile. One of the objectives was to characterize the seafloor morphology and the seepage activity across the mud volcanoes. The seepage activity was dominated by emissions of methane and heavier hydrocarbons associated with a major thermal contribution. The most active parts of the mud volcanoes were highly gas-saturated (methane concentrations in the water and in the sediments, respectively, of several hundreds of nmol/L and several mmol/L of wet sediment) and associated with significantly high thermal gradients (at 10 m below the seafloor, the recorded temperatures reached more than 40 °C). Patches of highly reduced blackish sediments, mats of sulphide-oxidizing bacteria, and precipitates of authigenic carbonate were detected, indicative of anaerobic methane consumption. The chemosynthetic fauna was, however, not very abundant, inhibited most likely by the high and vigorous fluxes, and was associated mainly with carbonate-crust-covered seafloor encountered on the southwestern flank of Amon. Mud expulsions are not very common at present and were found limited to the most active emission centres of two mud volcanoes, where slow extrusion of mud occurs. Each of the mud volcanoes is fed principally by a main narrow channel located below the most elevated areas, most commonly in the centres of the structures. The distribution, shape, and seafloor morphology of the mud volcanoes and associated seeps over the Central Nile Deep Sea Fan are clearly tectonically controlled.