With growing instability of spatial and temporal precipitation variability and water supply in Taiwan, utilizing alternative water sources is one of the important trends in water resources development. Understanding that hyporheic water is one of the resources that has the characteristics of slow flow velocity, low turbidity, high water quality and low ecological impact, it has a great potential to be utilized. However, the researches about hyporheic water are mainly focused on the interrelationships between the hyporheic zone and its biological ecosystem. The researches about hyporheic water utilization are relatively insufficient and the potential water content can’t be effectively estimated. Therefore, the objective of this study is to propose an innovative procedure to investigate three-dimensional distribution of the hyporheic zone and measure the potential utilizing capacity in prototype well that intakes hyporheic water in southern Taiwan. We also made measurements in wet and dry seasons to see the time series change. In this study, we firstly proposed Ultra Low Frequency Electromagnetic Wave Remote Sensing Techniques (ULF-EW RS), underground remote sensing techniques that passively receives natural magnetotelluric signals and has higher precision than traditional geophysical prospecting methods, to investigate the hyporheic zone. Second, we estimated the volume of water content and calibrated the results with hyporheic exchange model. Finally, we use water level data from 5 wells near the prototype well to verify the results. The results show that by applying ULF-EW RS techniques, in most cases the hyporheic zones identified in the study successfully matched the ground true well data and model simulation results, which provides an effective way to evaluate hyporheic water in southern Taiwan.