Quantitative criteria for selection of tracers for assessment of mixing of wastewater and pristine water are proposed and evaluated for leakage from a wastewater effluent recharge system to nearby pristine water wells and the dilution of the effluents in a reclamation well by pristine water from the surrounding aquifer. Two molecular tracers were compared: carbamazepine, an organic drug whose refractory behavior was evaluated on-site, and chloride, a widely used conservative tracer. The mixing ratios and the corresponding uncertainty levels in their calculation were evaluated using actual field data. Uncertainty level analysis illuminates the effects of the analytical errors in the determination of trace micropollutants on one hand and the high level of chloride in the background on the other. Uncertainty level calculations revealed that chloride is a somewhat better tracer for the estimation of the dilution of wastewater by flow from a pristine aquifer, whereas carbamazepine is a much better tracer for the calculation of wastewater contamination of nearby drinking water wells. Surprisingly, we show that even when carbamazepine degrades to a large and unknown extent, it can still be used to estimate accurately the probability that a site is contaminated by a wastewater stream.