Cultural eutrophication has become the primary water quality issue for most of the freshwater and coastal marine ecosystems in the world. However, despite extensive research during the past four to five decades, many key questions in eutrophication science remain unanswered. Much is yet to be understood concerning the interactions that can occur between nutrients and ecosystem stability: whether they are stable or not, alternate states pose important complexities for the management of aquatic resources. Evidence is also mounting rapidly that nutrients strongly influence the fate and effects of other non-nutrient contaminants, including pathogens. In addition, it will be important to resolve ongoing debates about the optimal design of nutrient loading controls as a water quality management strategy for estuarine and coastal marine ecosystems.