The Ciliwung River is the potential water source for the people of Jakarta and Bogor. Rapid urbanization and industrial development have sparked severe problems in the water resources of the Ciliwung River. The potential pollutants increase as the river flows through residential, business, and industrial areas, where drainage and sanitation infrastructure are worse. Water is naturally tagged with natural tracers, such as temperature, electrical conductivity, chemical constituents, and environmental water isotopes (δ2H and δ18O). These proved valuable tracers to identify the origin of the water. This research aims to trace the origin of the Ciliwung River water using a stable isotope approach and physical parameters. Research methods are field surveys, laboratory analysis, and analytical studies—sampling at 12 points of river water for a physical parameter and 5 points for stable isotopes. The research results show that the water origin of Ciliwung’s is rainwater. The stable isotopes in the upstream area are smaller than those in the upstream area experiencing enrichment. Factors leading to enrichment are inputs from anthropogenic activities to water bodies from household, agricultural, and industrial pollution. The results of this research are helpful for the government and academics in designing Ciliwung River conservation policies.