Multi-regional water supply system, which installed for supplying multiple water demands, is characterized by large-sized, long-distance, tree-type layout. This system is vulnerable to long-standing service interruption when a pipe breaks is occurred. In this study, a numerical method is proposed to calculate drainage time that directly affects time of service interruption. To begin with, governing equations are formulated to embed the delayed drainage effect by the friction loss, and to resolve complicated connection of pipelines, which are derived from the continuity and energy equations. The nonlinear hydraulic equations are solved by using explicit time integration method and the Newton-Raphson method. The developed model is verified by comparing the result with analytical solution. Furthermore, the model’s applicability is validated by the examples of pipelines in serial, in parallel, and complex layout. Finally, the model is utilized to suggest an appropriate actions to reduce the deviation of draining time in the C transmission line of the B multi-regional water supply system.