Increased global trade and modern intercontinental transportation have made invasive species an increasingly prominent stressor of freshwater ecosystems. Invasive species risk assessments, which range from simple screening protocols that focus on species attributes and ecological requirements to rigorous analyses of infestation, have become an important component of environmental impact assessment. In this paper we present two recent case studies in which risk and decision methods were applied to non-toxicological environmental issues that are central to many aquatic ecosystem management programs. The first example reviews potential infestation by the zebra mussel, Dreissena polymorpha, on Bayou Bartholomew, located in southeast Arkansas, as a result of the proposed augmentation of low flow conditions by pumping water from the nearby and much larger Arkansas River. The second example presents a retrospective analysis of the results of transplanting fat pocketbook pearly mussels, Potarnilus capax, from an approximately 6-km reach of a drainage ditch in eastern Arkansas. The two examples presented herein indicate the potential for improving environmental decision-making in the face of uncertainty-but in the presence of substantial information. As more rigorous attempts are made to widen and enhance applications of risk and decision methods to environmental decision-making, ecosystem management is likely to further improve.