The structures of microbial communities sign each environment and their dynamics sign the change of the environment. All waters (potable or dirty) are a microbial environment; as a consequence, microbial communities can sign them. This chapter show how a molecular fingerprint method, CE-SSCP, based on 16S rDNA gene can be applied as tool for water traceability. This chapter describes and explains clearly the SSCP technics and provides examples on spatial and temporal dynamics within three water networks. The examples present the potential of CE-SSCP for tracking cooling tower network, urban water network and ground water spring.