Agriculture is the main source of pollution in rivers and streams and this has a direct negative impact on human health. When pollutants from multiple sources to an agro-ecosystem occur, traditional techniques cannot help in evaluating the relative contribution of the different sources. Complementarily to conventional monitoring and mass balance approaches, stable isotopes of major biogenic elements (H,C,N,O and S) have the potential to characterize and quantify sources and transport of solutes through soil and water bodies in agro-ecosystems.