A soil column experiment was designed to investigate the response of an indigenous microbial population to a vertically fluctuating water table. A subsurface environment with a transitional zone was simulated. The water table in the soil columns was raised and lowered, and compared to columns under static conditions. Carbon dioxide and oxygen concentrations were measured. Peaks of CO2 occurred in the fluctuating columns immediately following a rise in the water table. Dissolved O2 in the fluctuating columns was consistently lower throughout the experiment, but these lower concentrations were exaggerated immediately following a rise in the water table. Values for total organic carbon in the pore water were slightly lower in the fluctuating columns. The results of this soil column study indicate that vertical fluctuation of the water table can enhance microbial activity of indigenous soil microbial populations. This increase in microbial activity suggests an increased rate of available carbon under these conditions.