Stable isotope (δ¹⁸O and δ¹³C) and SEM analyses were performed on 40 samples collected in the Upper Miocene (Messinian) evaporitic carbonate sequences (locally named Calcare di Base) of North Eastern Sicily. To recognize the carbonate parageneses less affected by post-depositional exchange phenomena that are representative of the paleoenvironment, the isotopic informations were integrated with SEM observations. The samples with extensive dissolution-reprecipitation evidences showed the most negative δ¹⁸O and δ¹³C values, while the samples having a relatively preserved micritic framework showed more positive values. In the literature concerning the Calcare di Base, the wide dispersion of the isotopic values has been interpreted as due to random syngenetic inputs of meteoric water in the depositional environment. Our results put forward the hypothesis that exchange processes in diagenetic or vadose-phreatic environment might also have happened.