This study evaluated the nitrogen compound removal efficiency of a hybrid subsurface constructed wetland, which began treating milking parlor wastewater in Hokkaido, northern Japan, in 2006. The wetland's overall removal rates of total nitrogen (TN) and ammonium (NH4+-N) improved after the second year of operation, and its rate of organic nitrogen (Org-N) removal was stable at 90% efficiency. Only nitrate (NO3−-N) levels were increased following the treatment. Despite increased NO3−-N (maximum of 3 mg-N/L) levels, TN removal rates were only slightly affected. Removal rates of TN and Org-N were highest in the first vertical bed. NH4+-N removal rates were highest in the second vertical bed, presumably due to water recirculation and pH adjustment. Concentrations of NO3−-N appeared when total carbon (TC) levels were low, which suggests that low TC prevented complete denitrification in the second vertical bed and the final horizontal bed. In practice, the beds removed more nitrogen than the amount theoretically removed by denitrification, as calculated by the amount of carbon removed from the system. This carbon-nitrogen imbalance may be due to other nitrogen transformation mechanisms, which require less carbon.