The biodegradation in the middle and downstream of slow-rate biological activated carbon (BAC) is limited by insufficient dissolved oxygen (DO) concentrations. In this study, a bubbleless aerated BAC (termed ABAC) process was developed by installing a hollow fiber membrane (HFM) module within a BAC filter to continuously provide aeration throughout the BAC system. The BAC filter without an HFM was termed NBAC. The laboratory-scale ABAC and NBAC systems operated continuously for 426 days using secondary sewage effluent as an influent. The DO concentrations for NBAC and ABAC were 0.78 ± 0.27 and 4.31 ± 0.44 mg/L, respectively, with the latter providing the ABAC with greater electron acceptors for biodegradation and a microbial community with better biodegradation and metabolism capacity. The biofilms in ABAC secreted 47.3% less EPS and exhibited greater electron transfer capacity than those in NBAC, resulting in enhanced contaminant degradation efficiency and long-term stability. The extra organic matter removed by ABAC included refractory substances with a low elemental ratio of oxygen to carbon (O/C) and a high elemental ratio of hydrogen to carbon (H/C). The proposed ABAC filter provides a valuable, practical example of how to modify the BAC technology to shape the microbial community, and its activity, by optimizing the ambient atmosphere.