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The objective of this study is to evaluate the use of the Analytical Element Method (AEM) toward multiobjective, multiscale, ongoing modeling needs at complex hydrologic sites such as those managed by the US Department of Energy. This method presents several advantages over the traditional numerical methods that include absence of grid, natural incorporation of hydrologic features, and generation of an exact solution at every point in a flow field. The AEM with its semi-analytical formulation is particularly efficient in addressing what-if scenarios, the resolution of boundary conditions, and the incorporation of new data all of which are important aspects of remediation efforts in complex sites. Our model accounted for important hydrologic features in an area of the Savannah River Site, South Carolina that included river branches, artificial surface basins, monitoring wells, and the existence of heterogeneities. Our simulated heads were found to be in excellent agreement with the measured heads, with over 90% of the wells exhibiting a maximum discrepancy of less than 10 ft. The AEM was found to be a very efficient and fast method for the analysis of a flow field even when a limited number of elements was considered. The AEM was seen to lead to better physical understanding and resolution of the critical components of a groundwater system and it can offer significant advantages in using models to guide site characterization and remediation efforts.