Nitrification and denitrification kinetics in sediment perfusion cores were numerically modeled and compared to experiments on cores from the Shingobee River MN, USA. The experimental design incorporated mixing groundwater discharge with stream water penetration into the cores, which provided a well-defined, one-dimensional simulation of in situ hydrologic conditions. Ammonium (NH₄⁺) and nitrate (NO₃⁻) concentration gradients suggested the upper region of the cores supported coupled nitrification–denitrification, where groundwater-derived NH₄⁺ was first oxidized to NO₃⁻ then subsequently reduced via denitrification to N₂. Nitrification and denitrification were modeled using a Crank–Nicolson finite difference approximation to a one-dimensional advection–dispersion equation. Both processes were modeled using first-order reaction kinetics because substrate concentrations (NH₄⁺ and NO₃⁻) were much smaller than published Michaelis constants. Rate coefficients for nitrification and denitrification ranged from 0.2 to 15.8 h⁻¹ and 0.02 to 8.0 h⁻¹, respectively. The rate constants followed an Arrhenius relationship between 7.5 and 22 °C. Activation energies for nitrification and denitrification were 162 and 97.3 kJ/mol, respectively. Seasonal NH₄⁺ concentration patterns in the Shingobee River were accurately simulated from the relationship between perfusion core temperature and NH₄⁺ flux to the overlying water. The simulations suggest that NH₄⁺ in groundwater discharge is controlled by sediment nitrification that, consistent with its activation energy, is strongly temperature dependent.