Distinguishing municipal wastewater effluent (MWWE) from other industrial effluents or through an urbanized watershed can be challenging. In complex receiving environments, linking environmental responses to specific compounds or effluents is not always straight forward. In order to characterize the inherent complexity of tracing MWWE in aquatic systems influenced by multiple stressors, a proposed multi-tracer suite is intended to highlight areas of potential biological concern. Characterization and quantification of effluent exposure to aquatic biota in this manner is essential to shape policies intended to encourage wastewater infrastructure development (i.e. treatment plant upgrade) and broader environmental management. This paper describes the use of a comprehensive suite of tracers that includes isotopes in support of a core surveillance program, demonstrating its effectiveness both empirically and with respect to diagnostic value contributed to monitoring programs.