Abstract This study investigated the discrepancies in nitrogen removal and clogging for vertical flow constructed wetlands (VFCWs) using different packing strategies. Parallel lab-scale VFCWs reactors were created and packed with quartz sand filter media. Three packing strategies were adopted: increasing-sized (I-packing), decreasing-sized (D-packing) and uniform-sized (U-packing) packing. The clogging rate coefficient and biomass accumulation rate were defined to assess clogging. The results demonstrated that the nitrogen removal was highest for the I-packing reactor at 43%. The ammonia and COD removal rates reached 56% and 64%, respectively. I-packing reactor presented an aerobic-to-anoxic transition area, where DO ranged from 4.6 to 0.3 mg/L. Such condition is ideal for the nitrification and denitrification reaction. Clogging is primarily the result of the rapid reduction of the effective porosity due to bio-film growth. Clogging is related to the position of biomass accumulation, while the reduction of the internal void space is not the determining factor for the I-packing reactor. The clogging rate of the I-packing reactor much lower than D-packing and U-packing reactors. Bed resting between operations can be used for clogging mitigation and system recovery, but this approach was not effective for D-packing. The I-packing reactor was proven to be the most efficient for nitrogen removal and showed the strongest clogging prevention capability.