Improving kinetic modeling of nitrification in rivers is of growing importance due to yearly increases in the anthropogenic release of nitrogen into rivers around the world. The use of water quality models can abate the expense of water quality monitoring while enabling the user to predict trends of variation. Data collected from a series of laboratory kinetic experiments were used to calculate the rate of nitrification in the Rideau River, Canada, and modify nitrification algorithms used in the traditional water quality model Qual2E. The modified model relates the reaction rate coefficients with a simple biomass concentration measurement of volatile suspended solids (VSS) in the river and subsequently introduces biomass growth functions directly into the kinetic algorithm. Furthermore, this modified model includes a nitrate-nitrogen assimilation pathway. The modified model demonstrates an improved correlation to nitrogen parameters observed in river water samples compared with the classical water quality model Qual2E. The inclusion of bacterial concentrations based upon the simple measurement of VSS plays a critical role in the reactions of the nitrification system and nitrate-nitrogen assimilation is an important pathway at low ammonia-nitrogen concentrations.