In order to predict fate and transport of nitrogen in soils, we described major nitrogen transformations and conducted flow and transport simulations using the HP1 (HYDRUS-1D and PHREEQC) program. Nitrogen transformations were described with first-order chain reactions for ammonification from organic matter, nitrification from ammonium, denitrification from nitrate, and immobilizations from inorganic ammonium and nitrate to organic matter. In order to couple nitrogen and carbon cycles, a simple carbon cycle was also described as first-order decay processes from the soil organic matter to biomass and carbon dioxide. The immobilization rate was given as a function of the carbon-to-nitrogen (C/N) ratio. All the first-order kinetics equations for the carbon and nitrogen cycles described in PHREEQC were linked with water flow, root water uptake, solute transport, and passive root nutrient uptake in HYDRUS-1D using the HP1 program. Furthermore, active root nutrient uptake for ammonium and nitrate was implemented in the PHREEQC program.