Water systems (e.g., potable water, wastewater, and storm water systems) are regarded as "lifeline" infrastructure. Their disruption can cause cascading effects, influencing the economy of an entire region. Past hazard events show that water availability is crucial for minimizing the societal impact of such events and for recovery processes. To date, stochastic simulations of hazards events, and their direct and indirect physical damage to water system components, are typically not coupled with hydraulic simulations of functionality loss and restoration, including water quality, pressure, and flow throughout the network. This work presents a comprehensive approach to the modeling of water system resilience subject to a seismic event; however, the procedure is general and can be applied to other network systems and hazards. The model performs: (1) a baseline deterministic hydraulic analysis on an undamaged water system, focusing on meaningful functionality metrics, (i.e., water pressure, quantity, and quality); (2) a probabilistic analysis of the damaged system considering the damage state and the performance level of each component; (3) a probabilistic analysis of the water system functionality, considering the physical damage analysis and the recovery time of each component.