People in remote areas are still drinking surface water that may contain certain pollutants including harmful microorganisms and chemical compounds directly without any pretreatment. In this study, we have designed and operated a pilot-scale drinking water treatment unit as part of our aim to find an economic and easily operable technology for providing drinking water to people in those areas. Our small-scale treatment unit contains filtration and disinfection (UV–C irradiation) stages to remove pollutants from source water. The water quality index was determined based on various parameters such as pH, temperature, dissolved oxygen, nitrate, nitrite, ammonium, phosphorus, dissolved organic carbon and bacteria. Water and media samples after DNA extraction were sequenced using Illumina MiSeq throughput sequencing for the determination of bacterial community composition. After the raw water treatment, the reduction of bacteria concentration ranged from 1 to 2 log10. The average removal of the turbidity, ammonium, nitrite, phosphorus and dissolved organic carbon reached up to 95.33%, 85.71%, 100%, 28.57%, and 45%, respectively. In conclusion, multiple biological stages in our designed unit showed an improvement of the drinking water quality. The designed drinking treatment unit produces potable water meeting standards at a lower cost of operation and it can be used in remote areas.