Many caves in Sicily have been shown to have a sulfuric acid or other hypogenic origin. We studied three caves (Palombara, Scrivilleri, Monello) near Syracuse (eastern Sicily), in an area that was strongly uplifted and faulted, creating multiple Pleistocene marine terraces. Mineralogy, stable isotopes and dating methods (paleomagnetism, U/Th) were used to characterize cave sediments, some of which were related to the initial hypogenic phase (Fe and Mn oxides, calcite spar), others were introduced by surface runoff later. Many other sediments are the result of in situ weathering, such as lime sands produced by condensation-corrosion processes on the calcarenite walls. Phosphates, kaolinite and montmorillonite are related to bat guano decay. Stable isotopes show that the speleothems derive from surface seepage with temperatures similar to the present, with no evidence of a hydrothermal origin. Other deep sources of aggressivity are also excluded. We obtained an age of 603 ka for a marine notch deposit near Palombara, as well as a possible paleomagnetic inversion (>780 ka) for clastic allogenic sediments. These ages are discussed, raising the question of the reliability of calculations extrapolated from marine terrace dating and the possibility that the caves may be older than expected. Cave morphologies clearly indicate a hypogenic phase, with aggressive ascending flows creating the typical Morphologic Suites of Rising Flow (MSRF). The bubble trails and acid notches are formed by carbonic degassing and subsequent acidification in more or less closed aerated environments at the water table. Carbon dioxide probably derived from both the bedrock and the oxidation of surface-derived organic carbon at the density boundaries of the freshwater lens. We propose a mixed Flank Margin Cave and hypogenic speleogenesis model, where dissolution was favored in areas of greater CO2 concentration, producing phreatic maze patterns recording past sea-level positions. We suggest that aggressiveness of the rising fluids could have partly originated at a shallow depth, in the mixing zone between fresh and salt water.