A first-time chemometric study of energy-dispersive X-ray (EDX) data of Charophyta gyrogonites is presented. Specimen provenance is a microbialitic carbonate lacustrine succession from the Triassic (Anisian, 243.8 ± 1.9 Ma) of the Cerro Puntudo Formation, San Juan, Argentina. Gyrogonites from three different strata of the succession are studied. Data obtained by EDX include major and minor components, which are analyzed by principal component analysis (PCA). The aim of this study is twofold: first to determine the preservation features of gyrogonites by way of a chemometric approach (i.e., EDX followed by PCA) and then to infer the likely, original chemical composition of the paleolake inhabited by charophytes. EDX spectra show the presence of O, Ca, and minor elements (e.g., Si and Mg), indicating a predominantly calcium carbonate (CaCO3) composition. Principal component analysis supports differences obtained between central and peripheral areas of the gyrogonites, indicating a higher CaCO3 content in their central part. On the other hand, in their outer part, the CaCO3 diminishes and the presence of Si compounds is recorded. No significant differences among gyrogonites from the three different strata are found, implying a similar preservation mode. This suggests a differential diagenetic pattern for the external cells of the gyrogonites than their centers. These results have implications regarding the chemical composition of the paleolake water (Si and Ca availability) and the provenance and catchment areas. Results are encouraging regarding the usefulness of a chemometric approach for studies of fossil remains in lacustrine environments when other techniques of chemical analysis are not available.