Biological activated carbon (BAC) biofilter coupling ultrafiltration (UF) is a promising process for the treatment of river water contaminated by pharmaceutical and personal care products (PPCPs). However, the pilot-scale study should be conducted to reveal the long-term removal performance and the respective contributions of BAC and UF. In this study, a BAC-UF system with treatment capacity of 0.16 m3 h−1 was operated for 130 days. The water quality was analyzed in terms of CODMn, UV254, NH4+-N, and PPCPs. The results showed that both BAC and UF were related to the removal of organic matter (CODMn and UV254), achieving the removals of 56.00% and 55.25%, respectively. Similarly, BAC and UF were both relevant to the removal effects of ammonia nitrogen, nitrite, and nitrate. Moreover, the BAC-UF process was featured with a high efficiency in the removal of PPCPs, and the average removal of total PPCPs reached 47.84%, especially anhydroerythromycin, sulfachloropyridazine, sulfadiazine, trimethoprim, and caffeine. Besides, it was found that the BAC unit played a key role in PPCPs removal and the UF unit also degraded them by the biomass on UF membranes. Therefore, this study proved the removal performance of BAC-UF for treating popular pollutants from river water, and the BAC-UF process in this work can be considered as a feasible method of producing clean drinking water.