A low energy nitrogen removal wetland system is disclosed to provide high rates of nitrogen removal treatment for wastewater with low energy requirements. The wetland system uses down-flow rock-filled wetlands for nitrogen removal. The system has no aeration requirements, thus resulting in low energy consumption. The wetland system comprises a first column receiving drainage influent, a mid-level reservoir, a second column receiving drainage from the mid-level reservoir and a lower level reservoir receiving discharge from the second column. The first and the second columns are filled with media layers comprise rock media with ammonia adsorption capacity for ammonia removal. The wetland system operates in a flood and drain operation mode or a continuous flow mode.