Integrated solutions to groundwater management problems require effective analysis of stream-aquifer connections, especially in irrigated semi-arid regions where groundwater pumping affects return flows and causes streamflow depletion. Scientific research can explain technical issues, but legal and management solutions are difficult due to the complexities of hydrogeology, the expense of data collection and model studies, and the inclination of water users not to trust experts, regulatory authorities, and in some cases, their management organizations. The technical, legal, and management issues are reviewed, and experiences with integrated management of stream-aquifer systems are used to illustrate how governance authorities can approach engineering, legal, regulatory, and management challenges incrementally. The situations in three basins of the State of Colorado with over-appropriated water resources are explained to identify modeling and control issues confronting regulators and managers of water rights. Water rights administration in the state follows the strict appropriation method and a workable technical-legal approach to establishing regulatory and management strategies has been developed. The explanations show how models and data management are improving, but the complexities of hydrogeology and institutional systems must be confronted on a case-by-case basis. Stream-aquifer systems will require more attention in the future, better data will be needed, model developers must prove superiority over simpler methods, and organizational arrangements will be needed to facilitate successful collective action amidst inevitable legal challenges. Continued joint research between technical, legal, and management communities will also be needed.