The aim of the study was to evaluate the nitrogen removal and its effects on the plant’s growth and leaves morphology. using two subsurface vertical flow (VF bed), with different depths (0.24 m2 × 0.70 m; 0.24 m2 × 0.35 m) and nitrogen load increments. The VF bed were planted with Vetiveria zizanioides, filled with light expanded clay aggregates (Leca®NR 10/20) and fed in parallel mode with synthetic wastewater. High ammonium nitrogen concentration ([NH4 + –N] from 68 ± 3 to 290 ± 8 mg L−1 ) was used without toxicity symptoms in plants, although the effects of ammonium nitrogen load were stopped the growth of the plants. Significant differences between ammonium nitrogen removed in each VF bed obtained for total nitrogen (TNinfl.) ≥ 27 ± 0.8 g m−2 d−1 . The nitrification was contributed to ammonium nitrogen removal because was found higher values of nitrate and nitrite in the effluent. These values were more higher in VF bed 1 than in the VF bed 2, since ammonium nitrogen removal were also more higher in VF bed 1 than in the VF bed 2. Total nitrogen mass balance was carried out and the results show that the nitrification/denitrification process occurred with nitrogen plants uptake. It was observed that the VF bed depth has an influence on all nitrogen removal processes. As higher the depth root system it is seemed to favour the creation of zones with different oxidations conditions that allow the nitrogen compounds to be removed intensively.