Water quality decay is an issue that negatively affects water supply companies' credibility. Therefore, they are required to implement policies that maintain water quality within acceptable levels; especially, when operation changes are made to the network. In order to do that, the use of water quality modeling as a process to understand the needs of the system is very useful. However, it requires a calibration process to guarantee that the results obtained from the model accurately represent what is occurring in the system. This paper presents a case study in which an automated methodology for the calibration of a water quality model based on a route followed by the water and the characteristics of the pipes that comprise it is tested in Bogotá's trunk network. Then, the process to develop the water quality model, taking into account the characteristics of the water quality sources and mixing models in storage tanks, is presented. The methodology was effective by accurately representing the process in the network, allowing the establishing of zones where the chlorine decay was significant, and determining the factors that affect its decay. As a result of this study, the Water Supply and Sewer Company of Bogotá (EAAB, Spanish acronym) has a calibrated water quality model used for different purposes such as the understanding of chlorine decay in district meter areas (DMAs) regardless of the operation scheme implemented on the trunk network. This facilitates establishing the optimal location for quality measurements.