Four vertical-flow CWs (VFCWs) with different substrates and aeration conditions were studied on nutrient-removal capacity from synthetic wastewater. Zeolite substrate VFCWs (none-aerated: VFCW-1, aerated: VFCW-3) paralleled with ceramsite (none-aerated:VFCW-2, aerated: VFCW-4) were used to study the removal efficiencies of N and organics, the bacterial community, and the related functional genes. The results indicated that the pollutant removal efficiency was significantly enhanced by intermittent aeration. VFCW-4 (ceramsite with aeration) demonstrated a significant potential to remove NH