In order to find the optimal running conditions and mechanisms of ammonia removal through a soil trench system that is designed for treating pretreated methane fermentation effluent, a soil column whose structure was similar to the soil trench system was prepared, and irrigated with wastewater below 30 degrees C. At the beginning, ammonia was mainly adsorbed by the soils, and the ammonia adsorption capacity of soils gradually saturated. After the 12th day, nitrification began in the soil column; the ammonia in the soil column decreased sharply, and the nitrite and nitrate peak appeared sequentially as the wastewater application rate decreased from 0.74 to 0.37 l h(-1). When the nitrification in the soil column reached a steady-state, 98% of all the ammonia in the influent was transformed into nitrate. By changing the running conditions such as temperature, aeration, and wastewater application rate, it was found that the ammonia removal efficiency can be improved by aeration and impeded by low temperature. In these three variables, wastewater application rate has much greater affect on the ammonia removal efficiency; a lower wastewater application rate can increase the ammonia removal efficiency substantially because of the longer travel time.