Over recent decades, the rural areas of Korea, including containing source waters, have become extensively developed. Combined sewer systems (CSSs) have been constructed to collect the sewage generated from these areas. Presently, it is common to experience localized heavy rain events, likely due to climate change, and sometimes, the volume of rainfall can become too high for a CSS to handle. In these cases, combined sewer overflow (CSOs) occurs, contaminating surface water, which may have been used as source water. Therefore, the Korean government will begin regulating the biochemical oxygen demand (BOD) of CSOs occurring during first flushes of less than 40 mg/L from 2024 onwards. In this study, a biofiltration-based technology was proposed to treat CSOs. Thus, this study aimed to remove BOD from CSO using this biofiltration system to contain cube-type media. For this, two different loading rates were tested on a pilot scale. Although the proposed system resulted in a footprint of only 10 % of that of a conventional activated sludge system, it was still capable of achieving efficient BOD removal. At a high loading rate, BOD removal efficiency was observed at approximately 53 %, and when this loading rate was reduced by 50 %, the removal efficiency was slightly improved to about 58 %. In both cases, the BODs of treated CSOs could be maintained below the proposed future standard: 31 mg/L and 28 mg/L for high and low loading rates, respectively. Therefore, the proposed system could potentially be preventing environmental contamination from COSs.