In this study, the biodegradation of a mixture of two trihalomethane (THM) compounds, chloroform (CF) and dichlorobromomethane (DCBM), was evaluated using two laboratory‐scale biotrickling filters (BTFs). The two BTFs, hereby designated as “BTF‐A” and “BTF‐B,” were run parallel and used ethanol as co‐metabolite at different loading rates (LRs), and a lipopeptide‐type biosurfactant that was generated by the gram‐positive bacteria, Surfactin, respectively. The results using BTF‐A showed that adding ethanol at a higher rate of 4.59 g/(m3 h) resulted in removal efficiencies of 85% and 87% for CF and DCBM, respectively. Conversely, for the same LR, the use of Surfactin without ethanol (BTF‐B) showed comparable removal efficiencies of 85% and 80% for CF and DCBM, respectively. The maximum rate constant for CF and DCBM for the BTF‐A was 0.00203 s−1 and 0.0022 s−1, respectively. For the same THMs LR, similar reaction rate constants resulted for the BTF‐B. Further studies were conducted to investigate and understand the microbial diversity within both BTFs. The result indicated that for BTF with co‐metabolite, Fusarium sp. was the most dominant fungi over 98% followed by F. Solani with less than 2%. F. oxysporum and Fusarium sp. were instead the dominant fungi for the BTF with Surfactin. Before introducing the Surfactin into the BTF, the batch experiment was conducted to evaluate the effectiveness of synthetic surfactant as compared to a biosurfactant (Surfactin). In this regard, vials with Surfactin showed better performance than vials with Tomadol 25‐7 (synthetic surfactant).