Freshwater environments are currently experiencing an alarming decline in biodiversity. As a result, scientists and managers must look for alternative management techniques to protect these aquatic systems. One such option that has potential to protect freshwater environments from numerous threats is the use of freshwater protected areas (FPAs). FPAs are portions of the freshwater environment partitioned to minimize disturbances and allow natural processes to govern populations and ecosystems. While similar conservation practices are well established in the terrestrial and marine environments, the use of FPAs for conservation of freshwater environments has been relatively slow. Despite this, numerous examples exist in which FPAs have been incorporated into successful management approaches for freshwater environments. In this paper, we outline some of the past success stories where FPAs have been used to protect freshwater environments, discuss some of the reasons that this technique has not proliferated to the same degree as marine protected areas, and present some of the challenges that managers and scientists must overcome if they wish to implement FPAs. We recommend that the term Freshwater Protected Area be adopted to such conservation efforts, thereby standardizing terminology and facilitating literature searches and dissemination of research findings. Furthermore, we encourage freshwater scientists, conservationists and managers to develop and implement FPAs in innovative and creative situations thereby permitting the growth of the research base for this valuable conservation technique.