Nitrate leaching from the agricultural fields to the surface water via subsurface drainage systems is one of the disadvantages of these systems. As these nitrogen losses often lead to the pollution of both surface and groundwater, they are likely to result in environmental degradation that will be detrimental to aquatic life, plants, animals, and humans. There are some traditional methods for nitrogen removal such as biological processes, chemical processes and physical operation. Recently, the biological processes have proven to be the most economical, feasible and efficient method for nitrogen removal. Furthermore, this method is the most promising method available for removing nitrate from water in the saturation conditions. Since subsurface soils are generally limited in the amount of available organic carbon, most microbial denitrification processes require additional carbon sources to sustain these activities. In this study, barley straw was used as a carbon source to enhance the denitrification processes and the effect of that on effluent nitrate and ammonium were evaluated. Two forms of position of this biofilter near the drainage pipe to remove the nitrate form the drainage water were investigated in the laboratory study. The results showed 60% of influent nitrate was removed by these two forms of position over the study period. These biofilters also could remove more than 85% of influent nitrate after 8 weeks. Also, the results showed that this treatment had reduced the effluent nitrate concentrations below the USEPA maximum contaminant level for drinking water of 45 mg L-1 nitrate at the end of the study.