The adsorption characteristics of various filter media and treatment efficiency of small pilot-scale constructed wetlands (CWs) were investigated in order to design optimum CWs for treating greenhouse wastewater. Calcite was the best filter medium for the adsorption of ammonium nitrogen and phosphorus under various temperature and pH conditions. However, removal efficiency of calcite for total nitrogen (T-N) removal was low due primarily to high nitrate levels. Thus, several hybrid CWs (containing calcite as filter media) consisting of combinations of vertical flow (VF) and horizontal flow (HF) beds were evaluated for improving efficiency for T-N removal. Both 2- and 3-stage combinations of the VF and HF beds were tested. The optimum hybrid CWs was demonstrated to be a 3-stage combination of horizontal flow (HF)–vertical flow (VF)–horizontal flow (HF), which provided suitable conditions for both nitrification and denitrification, which improved removal of T-N in wastewater containing nitrate. In the HF–VF–HF 3-stage hybrid CWs, the reduction in chemical oxygen demand (COD), T-N, and total phosphorus (T-P) in the effluent were 95.1, 68.4 and 94.3%, respectively. The removal of COD, T-N and T-P in 3-stage HF–VF–HF CWs was rapid in order of VF (second stage) ≫ HF (first stage) ≫ HF (third stage), VF (second stage) ≫ HF (third stage) > HF (first stage) and VF (second stage) ≫ HF (first stage) ≫ HF (third stage), respectively.