Hydropower use is responsible for a wide range of environmental disturbances to river systems. Over the past decades, aquatic science research has been successful in identifying a considerable number of relationships that exist between plant operation and ecosystem quality. This increase in scientific knowledge was, however, not matched by a corresponding reduction in environmental impacts stemming from hydropower. In the present paper, we show how aquatic science projects may be defined and implemented to better link scientific knowledge with the resolution of environmental problems. We base our analysis on a major aquatic science research project in which an eco-label for "sustainable hydropower" (Green Hydropower) was developed for Switzerland. We first assess the state of aquatic science research on alpine river systems. The Swiss history of hydropower shows that the limited adoption of this knowledge was due to a severe coordination and action problem. The Green Hydropower project aimed at establishing an environmental product label for hydropower plant operation, which should help overcome these problems. It had to deal with two major challenges: the integration of widely differing knowledge stocks and the management of a network of diverse stakeholders operating in a conflict-laden political environment. By carefully dealing with these two problem areas, the project was finally able to define a scientifically-based and broadly-accepted standard for Green Hydropower operation. We conclude by discussing lessons for the improvement of problem-oriented aquatic science research, in general.