Hot springs at the Beituo district, Taiwan are well-known for containing a significant amount of white or blue sulphur. With strong acidity and high conductivity, the used hot springs water did not meet the effluent water quality standards of the sewerage system. Discharging without appropriate treatment has adversely deteriorated the water quality of nearby Huang Gang rivers and agricultural irrigation ditch. Electrokinetic separation, an advanced water treatment technology with the concept of “circularity of resources”, can separate and concentrate ions from water through an electric field. In this study, we investigated the feasibility of ions removal and neutralization from hot spring water by two different stacks of Electrokinetic separation. Stack A can successfully remove and recover ions from hot spring discharge with the concentrate of sulfate <72 mg/L in 30 min and promote pH to 3.5 in 60 min while Stack B with bipolar membrane has better performance for neutralization. With the obtained results, we evaluated the productivity and energy consumption of each system. Lastly, we compared the process performance of two electrokinetic separation systems from the aspects of engineering and economy.