The Formosan landlocked salmon is a critically endangered species also known as the Taiwanese ‘national treasure fish.’ In recent years, the fish was stocked into Rahaw Creek (upper Yusheng Creek, Yilan), where a sustainable group had been successfully rehabilitated. Lately, however, frequent stream fragmentation events in Yusheng Creek have prevented the fish from expanding their habitat, killing many as a result. To understand the reasons for the fragmentation and to improve rehabilitation, the research team installed six monitoring wells across a 500-meter fragmented reach to record temperatures and groundwater levels, which allowed them to understand surface water-groundwater interactions over different periods. The findings showed that compared to the perennial ones, the fragmented reach is of significantly higher streambed vertical hydraulic conductivity, causing the water to infiltrate the streambed at higher speeds. The findings also indicated that the vertical hydraulic conductivity was influenced by discharge, rainfall changes and the remains of dead diatoms. Most fragmentation studies focus on streams in semi-arid climates. This paper not only demonstrates the uniqueness of how mountain stream discharge in humid subtropical climates is affected by hydrological conditions and bioactivities, but also sheds light on the complexity of surface water-groundwater interactions by examining temporal variations in hydraulic conductivity.