The oldest rocks in the area are found outcropping in the Quichat canyon to the south of Cuetzalan.  These outcrops consist of metamorphic and igneous rocks (granites, shists and gneiss) of Permian to Triassic age that are contemporary with the Tezuitlan massif to the south..  Above these, sits a discontinuous layer of deltaic sediments (the Cauhaus formation), principally conglomerates but including shales, sandstones and greywackes, the composition of the clasts indicating a relation to the underlying metamorphics and volcanics most probably by erosion of the Tezuitlan massif during the early Jurassic.  During the middle Jurrassic the area became slowly submerged, indicated by a transition from the Cauhaus to a sequence of black limestones  between 100 and 150m thick (the Taman formation). The nature of these limestones along with numerous chert bands, abundant ammonite fossils and occasional shale interbeds indicate the formation of a deep basin during this period. Deposition continued in this deep basin throughout the Jurassic and into the Cretaceous, the top of the Taman being marked by a transition to argillaceous limestones and calcerous shales (the Pimentia formation).   Above these lie a thick sequence of white limestones (the Tamaulpas formation). Formed during the early Cretaceous these limestones are thickly bedded but an abundance of chert nodules and continuous chert bands impede karst development.  Evidence from adjacent sites indicate that the area was once covered by Cretaceous deposits analagous to most of the Mexican karst areas, but these deposits are know completely eroded away.   Toward the Tertiary period the area was slowly tilted to the north.  In the north of the expedition area a sequence of calcerous sandstones covered by a layer of red sandstones indicating a transition from a marine to a coastal  enviroment during this period.

References:

Espinasa R,The Cave Systems of Cuetzalan: Geological Conditions of a Giant Karst Drainage Basin, Sociedad Mexicana de Explorations Subterraneas (SMES), Ingenieros No.29, 1993.