Ecological indicators play an important management role by helping characterize status and trends in ecological systems and diagnose causes of declining condition across a range of spatial and temporal scales. To better assess rivers and streams in Taiwan and encourage the nationwide applicability of a suite of environmental indicators, Bei-Gang River was chosen as a case study to determine how the environment of Bei-Gang River was degrading and how to possibly improve the river condition. The results of ecological survey and application of indicators indicated that the longitudinal connectivity could be improved by fishway passage construction. This study demonstrates a useful tool to give direction to mitigation efforts for improving river environment of future applications in Taiwan.