Compost and granular activated carbon biofilters operated at a wastewater treatment plant simultaneously removed low concentrations of hydrogen sulfide and volatile organic compounds. Through the use of phospholipid fatty acid analyses, the effects of declining pH caused by sulfide oxidation were established for microbial growth, microorganism stress, and microbial community structure. Microorganisms on both media demonstrated increases in microbial densities, varying degrees of environmental stress, and domination by gram-negative bacteria. However, the declining pH had little effect on compound removal, which was greater than 99% for the hydrogen sulfide and greater than 70% for the oxygenated and aromatic hydrocarbons. The microbial communities adjusted to difficult environmental conditions through acclimation of the species present or by growth of low-pH-tolerant species.