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Field and interpretive studies conducted by T.C. Winter and U.S. Geological Survey colleagues, and summarized in the 1998 publication “Groundwater and Surface Water – A Single Resource”, inspired a new generation of research centered on extensions of the groundwater-flow code MODFLOW to more sophisticated simulation of coupled groundwater and surface-water systems. Guided by emerging concerns with water availability, safe yields from wells, health of aquatic habitat, and climate change, the changes to MODFLOW involve: 1) the ability to more precisely and accurately represent the interface between surface and subsurface flows and 2) the consideration of a variety of mechanisms that influence their interaction. A review of the most important changes to the code is supplemented in this article by selected case studies in an effort to show the scope of the advances. The updates discussed include the Streamflow Routing (SFR), Lake (LAK), and Unsaturated-Zone Flow (UZF) Packages in MODFLOW-2005 and the Groundwater Management (GWM), Local Grid Refinement (LGR), and Newton (NWT) formulation versions of MODFLOW-2005. New developments feature the integration of rainfall-runoff modeling with MODFLOW in GSFLOW, coupling of GFLOW and MODFLOW in a hybrid code, and the forthcoming unstructured grid version of MODFLOW. They promise continued advances in the ability to use science to protect the single water resource.