This paper indicates the importance and advantages of the application of hybrid models in the control of water supply systems. A range of possibilities provided by this scientific approach is presented in the practical examples related to the fault diagnostics and fault-tolerant control in the pumping station (PS) control systems. It is presented that continuous monitoring and recording of the data of the pumping stations operation processes (electrical parameters such as electrical power, pressure or flow in the pipelines, water levels in the tanks, changes in various discrete states, etc.) could represent a significant resource that can be used to develop various hybrid models using the appropriate “data-driven” techniques. During this process, data are transformed into information, and thereafter, information into knowledge. Based on this knowledge, the control of PS operation can be significantly improved and a significant increase in the user’s satisfaction can be achieved while the maintenance and operation costs can be reduced.