Human activities have increased the input of bioavailable nitrogen into the rivers and streams across the world. This has caused harmful effects on ecosystem and human health, so that U.S. National Academy of Engineering has identified restoring balance to the nitrogen cycle as one of the 14 Grand Challenges facing engineers in the 21st Century. Biogeochemical processing of nitrogen in the hyporheic zone of streams, on the other hand, is thought to be an effective pathway for removing excess nitrate in these systems. In this thesis, I used a previously published method, called PASS model, to calculate direct denitrification velocity of nitrate ( vf,Dw ), which is defined as the ratio of the flux of nitrogen gas generated by direct denitrification and in-stream concentration of nitrate. I aimed to calibrate PASS model parameters and validate its results with a well-known set of data that was collected as part of the second lotic intersite nitrogen experiment (LINX II) across 72 streams in the United States. Altogether, I calibrated four fundamental parameters of the PASS model, including hyporheic exchange flux coefficient ( a ), rate constant of dissolved organic carbon mineralization ( Rmin,0 ), nitrification rate constant ( kNI ), and denitrification rate coefficient (κ ). I interpreted the results of the calibration by using Multiple Linear Regression (MLR) and Bootstrap techniques. At the end I crossvalidated the results from the calibrated PASS model with the LINXII data, in terms of two indicating uptake velocities, namely oxygen and nitrate uptake velocities and I performed a model goodness analysis reporting Nash-Sutcliff efficiency for each set of the model validation results.