This study compared two series of ecologically engineered treatment systems for nitrogen removal by enhancing nitritation and anammox. Each treatment series had two biofilters followed by one free-water surface (FWS) wetland. The first series included biofilters packed with marble chips and demonstrated a development process in nitrogen removal through the first 26 cycles of weekly batch operation. The series then stabilized at an average ammonium removal rate of 19.2 g N/m3 x d and total nitrogen removal rate of 10.6 g N/m3 x d during the latest 22 cycles. The second series, which consisted of biofilters packed with pea pebbles, experienced decreasing nitrogen removal rates. Anammox and heterotrophic denitrification accounted for 77% and 23%, respectively, of the total nitrogen removal in the marble biofilters. Nitrogen removal rates in the FWS wetlands increased significantly with ammonium loading rates increasing up to approximately 30 g N/m3.d. Ammonium and total nitrogen removal followed zero-order reaction kinetics. The marble biofilter-wetland series reached an ammonium removal rate of 30.3 g N/m3 x d and total nitrogen removal rate of 23.0 g N/m3 x d through the latest 22 cycles of batch operation at the average ammonium loading rate of 56.4 g N/m3 x d.