This article addresses a pressing issue concerning the attainment of required drinking water quality in municipal settings. The solution lies in optimizing the interaction among multiple elements involved in this process. The interaction encompasses the transport system with its geometric, physicochemical, and operational characteristics, as well as the transported medium, which is drinking water with its physicochemical, operational, and incrustation characteristics. This article provides an overview of the current state of piped water systems and explores the integration of factors influencing the formation of incrustation to minimize its occurrence. Special attention is given to the meticulous selection of factors that impact water quality, considering their advantages and limitations in the assessment. The optimization process relies on Saaty’s method of comparing individual factors and conducting a thorough multi-criteria analysis. The outcome of the analysis culminated in the development of a three-stage procedure for de-incrustation of pipeline systems. To ensure a comprehensive perspective, it is crucial to approach the entire issue in accordance with ISO 46001-compliant water management systems.