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The Itapema and Barra Velha formations are key carbonate reservoirs in the Pre-Salt section of Brazil’s Santos Basin. However, distinguishing the contact between these units during drilling operations is challenging due to the lack of clear diagnostic features in well logs and the fragmentary nature of cutting samples. This study introduces a geochemical approach using real-time X-ray fluorescence (XRF) analysis of calcium and strontium (Ca-Sr) in cutting samples to identify the Pré-Alagoas Unconformity, which separates the two formations. Results from 20 wells show that in 13 cases, the contact could be recognized by the divergence of Ca and Sr curves, with Sr levels increasing above the unconformity. This geochemical pattern reflects changes in paleoenvironmental conditions, notably increased salinity during the deposition of the Barra Velha Formation. The method’s reliability is enhanced by the integration of XRF with X-ray diffraction (XRD) analyses, although it may be affected by diagenetic processes such as dolomitization or contamination by barite. The Ca-Sr technique proves to be a useful, real-time tool for stratigraphic identification during drilling operations in Pre-Salt carbonates.