The fates of various nitrogen species were investigated in a layered biological infiltration system under an intermittently wetting regime. The layered system consisted of a mulch layer, coarse soil layer (CSL), and fine soil layer (FSL). The effects of soil texture were assessed focusing on the infiltration rate and the removal of inorganic nitrogen species. The infiltration rate drastically decreased when the uniformity coefficient was larger than four. The ammonium in the synthetic runoff was shown to be removed via adsorption during the stormwater dosing and nitrification during subsequent dry days. Stable ammonium adsorption was observed when the silt and clay content of CSL was greater than 3%. This study revealed that the nitrate leaching was caused by nitrification during dry days. Various patterns of nitrate flushing were observed depending on the soil configuration. The washout of nitrate was more severe as the silt/clay content of the CSL was greater. However, proper layering of soil proved to enhance the nitrate removal. Consequently, a strictly sandy CSL over FSL with a silt and clay content of 10% was the best configuration for the removal of ammonium and nitrate.