When soil columns were operated aerobically on a flooding-drying schedule in a previous study, good removals were observed for several organic compounds at concentrations ranging from 1 to 1,000 micrograms per liter in primary wastewater. In this study, fractional breakthroughs of most compounds increased substantially once operating parameters were modified and the soil became anaerobic. These results imply that microbial removal of trace organic compounds can be inhibited if anaerobic conditions develop during rapid infiltration of wastewater.