A model that represents the behavior of a critical system or process, such as the drinking water treatment process, is vital for the evaluation of new procedures or their optimization without affecting the real system or risking the population, avoiding economic losses. Due to the complexity in the dynamics of drinking water treatment plants, the use of Coloured Petri Nets is recommended to model the behavior of the variables involved in the process. In this context, this work presents a structured procedure that allows to obtain a model considering a dynamic driven by the occurrence of discrete events and that allows the generation of useful information that can later be used to verify the effectiveness and efficiency of new operating strategies. To evaluate this proposal, a model of the drinking water treatment process of Puerto Mallarino located in Cali, Colombia was developed. Modeling, both the stages of the purification process, and the approximate behavior of the variables involved under the assumption that the changes obey only to the intensity of the raining season.