Hydrologic systems are strongly influenced by interacting processes that from pore space to watershed scale, but it remains a challenge to describe, model, and observe these processes at high resolution in the field. Recently, the Raman spectra distributed temperature sensing (DTS) for use in hydrologic application presents an opportunity for temperature measurements continuously in both space and time and provides a comprehensive picture of heterogeneity for the entire system. Chichiawan Watershed in Taiwan is the only habitat for the endangered species of Formosan land-locked salmon. However, the stream fragmentation, no surface streamflow, seriously reduced the salmon population, hampering the restoration work. Therefore, the utility of combining a high-resolution DTS with long-term monitoring data in the piezometers was to illustrate the complicated dynamics of hyporheic fluxes and to identify a suitable river restoration strategy to mitigate the effect of fragmentation on endangered salmon. The DTS measurements was conducted on the length of the 1,250 m reach covering the fragmented segment of creek from 7-13 November 2018 and seven installed piezometers provided the long-term water levels and streambed temperatures. The results showed that the propagation of stream fragmentation has been observed and the groundwater inflows has been clearly identified. The concentrated locations of groundwater inflows at the downstream confirmed the downstream channel is a perennial stream. The upwelling fluxes is differentiated from the regional groundwater and their contributed ratio vary with time and space. River restoration to mitigate the stream fragmentation can extend the habitat of salmon and the upwelling cold water can provide the thermal refuge for salmons during the summer.