The aim of this study is to develop a short cost-effective methodology for tracing the temporal and spatial anthropogenic inputs of micropollutants into ecosystems. The method involves a precise identification of the sampling sites based on various constraints: (1) one sampling site at each location to reduce the cost and the sampling time, (2) the sites are at sufficient mixing length from the release of micropollutants, and (3) they are identified with the aim to conduct mass balances. The methodology is applied to the identification, the quantification, and the distribution and transport of 21 emerging micropollutants in the Meurthe and Moselle river systems in the vicinity of the city of Nancy in France. The validity and reliability of the methodology is verified by using a mass-balance method at the confluence of the two rivers, where the mass fluxes upstream and downstream of the confluence compare well for nearly all the micropollutants. The methodology is employed to reveal mass fluxes of micropollutants discharged from the WWTP into the river water and point out the high efficiency of the drinking water treatment plant. The approach provides new insight into the identification of the sources of micropollutants in the rivers and the effects of hydrological and anthropogenic factors. The spatial anthropogenic inputs of micropollutants are highlighted in particular situations where discrepancies in the mass balance take place.