The purpose of this study was to completely remove low levels of 1,4-dioxane, a controlled substance with high solubility, low degradability, and high hazard level, from water using a specific microbe-immobilized carrier. A cell-entrapped carrier based on polyethylene glycol diacrylate was prepared using enriched culturing of Candidatus Saccharibacteria, using 1,4-dioxane as the only carbon source in activated sludge. When the 1,4-dioxane concentration was 5 mg/L, the cell-immobilized carrier process removed up to 0.026 mg/L of 1,4-dioxane at a hydraulic retention time (HRT) of 6 h, but the activated sludge process was removed up to 0.12 mg/L at an HRT of 20 h. The mollifying effect created by internal recirculation was less effective than that of HRT. This technology could be a cost-effective alternative to advanced oxidation process for the treatment of landfill leachate and groundwater contaminated with 1,4-dioxane.