Although lava-rock-based biofilters have demonstrated their efficiencies for hydrogen sulfide (H2S) removal found in odorous air emissions, the biogeochemical basis for this removal is unclear. In this study, samples of lava rock and rinse water from biofilters at Cedar Rapids Water Pollution Control Facilities (Iowa) were used to study the structure and chemical composition of lava rock and to identify the predominant microorganism(s) present in lava-rock-based biofilters. It was found that iron, in the form of Fe2+ and Fe3+, was present in lava rock. Although literature suggests that Acidithiobacillus thiooxidans are primarily responsible for gaseous H2S removal in biofilters, our study showed that Acidithiobacillus ferrooxidans was the dominant microorganism in the lava-rock-based biofilters. A novel mechanism for H2S removal in a lava-rock-based biofilter is proposed based on the biogeochemical analysis of lava rock.