The geochemical data were measured from a 57-cm-long sediment core retrieved from Lake Alchichica (19° 24' 38 N, 97° 24' 14 W, 2322 masl) at a water depth of ~ 60 m using a Uwitec® coring device equipped with a 9-cm coring tube. Geochemical compositions of the sediment core were analyzed using an ITRAX X-ray fluorescence core scanner (CS-XRF) at the INRS Centre Eau Terre Environnement in Canada. The analysis produced the ratio of Compton (incoherent) to Rayleigh (coherent) scattering (Inc/Coh), which can serve as an indicator of sediment organic content. The scans were measured at 2 mm intervals using 20 kV with a current of 10 mA and a dwell time of 20 seconds. To reduce matrix effects and address the closed-sum issue, elemental intensities (measured in counts per second) were transformed using the centered log-ratio (clr) method. For better visualization, all elemental data were subjected to min-max normalization.