Biofilters are widely used for treating various types of wastewater and also recently in controlling non-point source (NPS) pollution including piggery stormwater. Gravels are common substrates employed in this type of biofilters. In this study, three parallel woodchip based biofilters with different thickness of woodchip layer were constructed and operated for about 300 days in 2013. Sampling was conducted every 2 days. The water temperature, pH, electric conductivity (EC), turbidity and DO were measured in situ. Other water quality parameters were analyzed in accordance with the Standard Methods for the Examination of Water and Wastewater (APHA et al. 1995). On one hand, with less woodchip media packed in the biofilter, better removal of TN, TP, NH4-N, TCOD was achieved. On the other hand, almost all NO3-N were removed regardless of the thickness of woodchip. In addition, with deeper thickness of woodchip media in the biofilter, more increased alkalinity and released organic matters were observed at the effluent. Alkalinity is important in biological nitrogen processes, especially in the reactions of ammonia transformation into nitrate (nitrification). Organic matters released from woodchip served as the carbon source to derive denitrification. It seems that only small amount of the woodchip were sufficient to achieve nice removal of nitrogen and phosphorus. Therefore, the amount of the woodchip could be a key in designing a woodchip biofilter.