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The Fayum Depression of Egypt has produced a great diversity of fossil material, including marine and freshwater fishes. In contrast to the Eocene formations of the Fayum, the Oligocene Jbel Qatrani Formation has been more or less consistently considered to be deposited in a freshwater environment; however, the ichthyofauna indicates a more complex picture. Cenozoic fishes have been convincingly used to interpret the palaeoenvironment in which sediments were deposited. Based on the elasmobranch and osteichthyan faunas of the Jbel Qatrani Formation, we interpret that this formation was not deposited entirely in fresh waters, but had some marine influence, particularly in the lower part of the formation. The mixture of freshwater elements, such as polypterids and alestids, with brackish and marine elements, including myliobatid stingrays, in the Quarry E site suggests a local palaeoenvironment that was very close to the shoreline, in a less protected area, or under more seasonal influence than the rest of the sites in the formation. Additionally, the early Oligocene elasmobranch fishes from Quarry E have a strong biogeographic relationship with sites in Oman and Pakistan, in the eastern Tethys, representing a restricted fauna possibly limited in distribution by cooling global temperatures.