This paper uses observed daily streamflow data to examine the flow regime alteration and how these changes might potentially affect freshwater ecosystems. The earth surface temperature has been observed gradually increase and associate with precipitation and atmospheric moisture changes over space and time. Climate induced flow regime changes are examined by Indicators of Hydrologic Alteration approach. The annual extreme water conditions (1-, 3-, 7-, 30-, 90- day annual minima or maxima) reveal larger alteration from analyzing twenty-three gauging stations throughout Taiwan. More severe flood and drought events happen in the period of after 1991 than the period of 1961-1990. Frequency and duration of the flood and drought events also reveal high fluctuation. Flow regime is being altered and is going to continue into the foreseeable future. The aquatic organisms not only need to defend themselves from the anthropogenic damage to the river system but also are facing the on-going threat from thermal and flow regime altering under changing climate. This paper tries to raise this issue to allow water resources managers taking some precautionary measures to reduce the cumulative effects from anthropogenic influence and changing climate.