Biological activated carbon (BAC) filtration is usually considered to be able to decrease formation potentials (FPs) of disinfection by-products (DBPs) in drinking water treatment plant (DWTP). However, BAC filters with long running time may release microbial metabolites to effluents and therefore increase FPs of nitrogenous DBPs with high toxicity. To verify this hypothesis, this study continuously tracked BAC filters in a DWTP for one year, and assessed effects of old (running time 8–9 years) and new (running time 0–13 months) BAC filters on FPs of 15 regulated and unregulated DBPs. Results revealed that dissolved organic carbon (DOC) removal was slightly higher in the new BAC than the old one. All fluorescent components of dissolved organic matter evidently declined after new BAC filtration, but fulvic acid-like and soluble microbial product-like substances increased after old BAC filtration, which could be caused by microbial leakage. Correspondingly, new BAC filter generally removed more DBP FPs than the old one. 46.5% HAA7 FPs from chlorination and 44.3% THM4 FPs from chloramination were removed by new BAC filter. However, some DBP FPs, especially HAN FPs, were poorly removed or even increased by the old BAC filter. Proteobacteria could be a main contributor for DBP precursor removal in BAC filters. Herminiimonas, most abundant genera in new BAC filter, may explain its better DOC and UV254 removal performance and lower DBP FPs, while Bradyrhizobium, most abundant genera in old BAC filter, might produce more extracellular polymeric substances and therefore increased N-DBP FPs in old BAC effluent. This study provided insight into variations of DBP FPs and microbial communities in the new and old BAC filters, and will be helpful for the optimization of DWTP design and operation for public health.