Smart Water Distribution systems (WDS) are vulnerable to cyber-attacks due to increased connectivity. Current simulation tools often lack full integration of cyber layers or fail to accurately represent real-world configuration of the cyber-physical layers. We present here WaCSim, an advanced simulation tool providing cyber-physical modeling for WDSs. WaCSim offers two primary enhancements First, WaCSim expands cyber-network configurations by incorporating three architectures (a) Programmble Logic Controler (PLC) simulates decentralized operations where PLCs communicate with each other over the network, sharing sensor data to operate collaboratively without central Supervising Control and Data Acquisition (SCADA) intervention; (b) SCADA Control that simulates SCADA system as a central controller, receiving data from all PLCs and invoking commands; (c) Hybrid Control that allows PLCs to receive data from other PLCs and from the SCADA. These three schemes enable the simulation of different configurations ranging from fully decentralized to fully centralized control schemes. Second, WaCSim provides a user-friendly interface for integrating customizable Python based algorithms that can be implemented with the Scada or PLCs. Users can implement Conflict Resolution Algorithms (CRAs) to handle discrepancies between PLC and SCADA commands, as well as algorithms for anomaly detection, optimization, and system control. This enables users to assess the impact of cyber-attacks and their mitigations within the simulation tool. We present case studies demonstrating how WaCSim can simulate cyber-attacks on different architectures and evaluate different mitigation strategies. These examples highlight WaCSim’s utility in enhancing the resilience, security, and operational efficiency of water distribution networks.