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Typically, computer-based tools built on mathematical models define the time-series behavior of contaminants, in dissolved or colloidal form, within the spatial boundaries of water distribution systems (WDS). EPANET-MSX has become a standard tool for WDS quality modeling due to its collaboration with EPANET. The critical challenges in applying EPANET-MSX include conceptualizing the exchanges among multiple reacting constituents within the WDS domain and developing the scientific descriptions of these exchanges. Moreover, due to its complicated user interface, the EPANET-MSX application demands programming skills from a software engineering viewpoint. The present study aims to overcome these challenges by developing a novel computer-based tool, EPANET-C. Via built-in and customizable conceptual and mathematical models’ directories, EPANET-C simplifies WDS water quality modeling for users, even those lacking programming expertise. Due to its flexibility, EPANET-C can become a de facto standard tool in WDS quality modeling study both for the industry and the academia.