Over the last few decades there has been increasing concern for the human impacts on river ecosystems. River managers are increasingly turning from hard engineering solutions to ecologically based restoration activities in order to improve degraded waterways. Although the concepts have been widely accepted by engineers in Taiwan, lack of engineer-friendly appraisal methods hindered further progress of river ecological engineering projects. In this study, we developed 'Environmental Matrix of Fish' as a quantitative tool to evaluate the change of aquatic habitat. Hsin-Dian Stream system was selected as the case study for verification. The results showed that this proposed matrix successfully captured the spatial and temporal change of the fish assemblage, and provided a better understanding of historical influences on fish community structure over watershed scale. The tool with its quantitative environmental factors can thus help engineers identify habitat requirements for the fish communities easily as well as support managing and improving river environment for future restoration applications in Taiwan.