Gasification is a promising method for extracting carbon from nearly all types of biowastes, producing gaseous products containing H 2 , CO, and CO 2 . This study demonstrates a novel combination of gas fermentation and water remediation. On the basis of a membrane biofilm reactor fed with a gaseous mixture of H 2 and CO 2 , the effective removal of nitrate (>99%, 0.44 g of N m −2 day −1 ) and perchlorate (>95%, 18.3 mg of Cl m −2 day −1 ) was demonstrated in a long-term experiment, together with the observed generation of volatile fatty acids (VFAs). A suite of batch experiments were conducted in situ and ex situ to reveal the mechanisms of the observed removals, which showed the tight coupling of in situ gas fermentation and contaminant removal. Specifically, the heterotrophic reactions using VFAs formed in gas fermentation played the dominant role in contaminant removal (>90%), while the autotrophic reaction driven by H 2 in the gas mixture contributed marginally (<10%). The examination of the microbial community showed the dominance of fermenting bacteria, such as Acetobacterium_unclassif ied and Sporomusa, and denitrifying bacteria, such as Comamonas, Dechlorobacter, and Pseudomonas. Together, these results lead to the proposal of an alternative to gaseous products from biowaste gasification to achieve effective removal of various contaminants in water systems.