A laboratory-scale vertical flow constructed wetland system was designed and monitored to compare nitrogen removal rates and pathways from both saturated and unsaturated zones under a hydraulic loading rate and influent total nitrogen concentration of 1.5 m3/m2.d and 508 mg/L respectively. Weekly measurements of the concentrations of nitrogen compounds, chemical oxygen demand, temperature, dissolved oxygen, oxidation-reduction potential, and hydrogen ion concentration were taken throughout the study. At the end of the experiments, PCR analysis of 16S rRNA gene sequencing was performed to identify microbial communities in the unsaturated and saturated parts of the system. The nitrogen compounds were removed from the system after 182 days, with similar total nitrogen removal efficiencies (94% and 93%) for the unsaturated and saturated zones respectively. Heterotrophic nitrification/aerobic denitrification was the major pathway responsible for the removal of nitrogen compounds. Adsorption into the gravel bed also contributed to ammonium removal. Proteobacteria were the dominant bacterial strains involved in nitrogen transformation and accounted for 80% of the total bacteria in the unsaturated zone and 60% in the saturated zone. With little difference in the concentration removal efficiencies of the unsaturated and saturated zones, a more effective design would be an entirely saturated wetland as the total mass removal of nitrogen depends on the water volume stored, which at full saturation in this design was seven times greater per unit wetland volume than the unsaturated zone.