This study examines the feasibility of tracing and quantifying the progress of different water sources along the water–effluent–SAT (Soil Aquifer Treatment) chain using 2H and 18O isotopes. The research was conducted at the Dan Region Reclamation Plant (Shafdan), which reclaims ~135 MCM/year of effluent for irrigation. Water samples representing different stages along the chain were taken in two surveys during 2010–2011 and 2014. δ18O and δ2H values were used for mixing ratios (MR) calculations, and compared with calculated MRs using chloride and carbamazepine concentrations. The results showed a relative enrichment of 18O and 2H in the Israeli water system compared to the regional groundwater, due to the addition of massive quantities of desalinated water. A linear correlation for δ2H vs. δ18O with a slope of 4.5 was found for the different freshwater sources and their mixing products, suggesting evaporation-mixing effects. MR values indicate on the spreading of new type of effluent originating from desalinated water in the aquifer. A dilution model explains the isotopic compositions in the water system and of the Shafdan effluents. Water isotopes have an advantage over other tracers, due to the ability to predict their ratio in the supply system and in the effluent, based on mass balance calculations and on knowledge of water supply volumes.