Water storage tanks are one of the primary and most critical components of water distribution systems (WDSs), which aim to manage water supply by maintaining pressure. In addition, storage provides a surplus source of water in case of an emergency. To gain the mentioned advantages, storage tanks are incorporated in most WDSs. Despite these advantages, storage can also pose negative impacts on water quality, thereby affecting water utilities. Water quality problems are a result of longer residency times and inadequate water mixing. This study aimed to construct a model of a tank’s water quantity and quality by formulating and solving governing equations based on inlet/outlet configurations and processes that influence the movement of water and chemical substances inside it. We used a compartment model to characterize the mixing behavior inside a tank. A water quality simulation model with different compartment arrangements was explored for extended filling and draining of storage, which was further validated using a previously published case study.