Bioaugmentation is a promising technology to enhance the removal of specific pollutants; however, environmental impacts of implementing bioaugmentation have not been considered in most studies. Appropriate methodology is required for the evaluation from both in-depth and comprehensive perspectives, which leads to this study initiating the application of life cycle assessment (LCA) of bioaugmentation. Two LCA methods (CML and e-Balance) were applied to a bioaugmentation case with the aim of illustrating how to evaluate the environmental impacts of bioaugmentation from different perspectives based on the selection of different LCA methods. The results of the case study demonstrated that the LCA methods with different methodology emphasis produced different outcomes, which could lead to differentiated optimization strategies depending on the associated perspectives. Furthermore, three important aspects are discussed, including coverage of impact categories, the selection of characterization modeling for specific pollutants, and the requirement of including economic indicators for future investigation.