Nitrogen (N) transformations and removal in integrated constructed wetlands (ICWs) are often high, but the contributions of various pathways, including nitrification/denitrification, assimilation by plants and sediment storage, remain unclear. This study quantified the contributions of different N removal pathways in a typical multi-celled ICW system treating domestic wastewater. Findings showed near complete average total N retention of circa 95% at 102.3 g m−2 yr−1 during the 4-year period of operation. Variations in total N and NH4–N removal rates were associated with effluent flow volume rates and seasons. According to the mass balance estimation, assimilation by plants and sediment/soil storage accounted for approximately 23% and 20%, respectively, of the total N load removal. These were the major N removal route besides microbial transformations. Thus, the combination of plants with high biomass production offer valuable opportunities for improving ICW performance. The retrieval and use of sequestered N in the ICW sediment/soils require coherent management and provide innovative and valuable opportunities.