In recent years, the interest in modeling complex engineering systems has grown rapidly. Due to their highly nonlinear nature coupled with their critical importance, the task of modeling such systems becomes a high-risk, high-payoff endeavor. There are many complexities associated with understanding and modeling the dynamics of such systems, these include functional, spatial and temporal complexities. The main objective of this paper is to present a modeling framework that enables the planning and evaluation of complex engineering systems taking into account these multidimensional complexities. The framework uses a multidimensional hierarchical decomposition of complex engineering systems combined with modeling techniques such as System Dynamics and Agent Based Modeling. Decomposition and modeling are integrated to simulate possible future states of the system and to evaluate different plans and scenarios for system evolution using key performance indicators (KPIs). The paper also presents a case study demonstrating the use of the proposed framework for an integrated water model applied to the kingdom of Saudi Arabia.