A regional modern river-sand geochemical mapping study in the majority of the Timor-Leste territory, including the research area, has not been previously reported. This study demonstrated the potential of modern river sand geochemical mapping as an effective method for lithological mapping, particularly in areas that face challenges in conducting efficient geological fieldwork and have limited geological information. A total of 53 modern river sand samples were collected and analyzed. Before examining the samples using wavelength-dispersive X-ray fluorescence for ten major elements, the loss-on-ignition method was employed. In the Clerec drainage basin, SiO2, CaO, and K2O showed positive correlations, and CaO was positively correlated with MnO. Similarly, in the Sahe River catchment, a positive relationship was observed between CaO, MnO, and TiO2. These findings suggested the presence of quartz, manganese, secondary K-bearing minerals, and secondary Ti-bearing minerals in carbonate rocks that have undergone silicification and other alteration processes. The principal component analysis results corroborated the SiO2/Al2O3 and K2O/Na2O ratios and the ICV findings. PC1 was related to the variations in Ca-poor and Ca-rich rocks; PC2 indicated notable inputs from SiO2-rich and SiO2-poor rocks; and PC3 revealed the possibility of contributions from secondary mineral assemblages related to silicification and low-grade metamorphic processes.