In cyber-physical systems (CPSs), embedded computing systems and communication capability are used to streamline and fortify the operation of a physical system. Intelligent critical infrastructure systems are among the most important CPSs and also prime examples of pervasive computing systems, as they exploit computing to provide "anytime, anywhere" transparent services. The existing body of knowledge includes techniques for assessment, modeling, and simulation of physical and cyber infrastructures, respectively, but such isolated analysis is incapable of fully capturing the interdependencies that occur when they intertwine to create a CPS. Fundamental differences exist between the attributes of cyber and physical components, significantly complicating representation of their behavior with a single comprehensive model or simulation tool. This paper articulates the challenges present in integrated simulation of a CPS, where the goal is to accurately reflect the operation and interaction of the cyber and physical networks that comprise the system. A solution is presented for the CPS domain of intelligent water distribution networks, using EPANET and Mat lab to represent the physical water distribution network and the decision support algorithms used to control the allocation of water, respectively.