The natural flow regime has become the dominant framework for environmental flow management, appearing in numerous technical and guidance documents, and showing how scientific concepts can profoundly influence policy implementation. Owing to the scarcity of water resources in many regions and growing demand, the need for science-based protection of environmental flows will become increasingly urgent. To protect flows for ecological uses, science and law are necessarily intertwined but the law is not uniform. It is location and case specific, which requires that the science be designed to address the applicable law. Protection of interstate water resources requires a precise showing that harm occurs to species of value when flows are diminished beyond a certain amount and for a certain duration. Protecting flows is multi-disciplinary. Hydrologists must show that flow declines are directly caused by human activity. Economists/sociologists must show that the ecological harm to the particular species causes a human hardship. Using a case study of a failed effort to apportion flows between Georgia and Florida, we illustrate the challenges in demonstrating harm and remedy in a highly contested dispute over interstate water use. State law often provides much greater clarity to obtain flow protection but similarly requires scientific support before such protection will be granted by the state water agency. At least 13 states allow for some level of instream flow protection, but generally differ in evidence required for an application to be granted. Other states may lack specific statutory guidance and hence provide less clarity on how an application for instream flows can be argued. Few instream flow applications have been granted without litigation, and for that reason, the scientific and economic evidence needs to be focused on the specific criteria for granting a permit. Among the exceptions have been the Loup, Elkhorn, and Niobrara Rivers in Nebraska – a state with some of the most detailed statutory criteria. These examples illustrate some common challenges with establishing instream flow rights.