Plants and their associated microbes can be used in the cleanup and prevention of environmental pollution. This relatively new and growing technology uses natural processes to break down, stabilize, or accumulate pollutants. Knowledge of the biochemical processes involved may lead to the development of more efficient plants and better management practices. One approach for improving the efficiency of phytoremediation includes developing transgenic plants. Here, we give an overview of phytoremediation methods and their associated biological processes, and discuss approaches that have been used successfully to breed transgenic plants with advanced phytoremediation properties. Much is still unknown about the ecological implications of phytoremediation, especially when using transgenic plants. Phytoremediation-related processes can change the location or chemical makeup of contaminants; the question is how those processes will affect the interactions among organisms in the ecosystem, and how transgenic plants might influence these relationships. Continued multidisciplinary studies will result in a better understanding of the ecological interactions that contribute to phytoremediation, the effects of phytoremediation on ecological relationships, and the movement of pollutants through ecosystems.