Discharge of organic waste results in high nutrient pollution of the water bodies which is a major menace to the environment. A high quantity of nutrients such as ammonia causes a reduction in the dissolved oxygen level and induces algal growth in the water bodies. Water quality models have been the tools to evaluate the rate at which streams can disperse the pollutants they receive. Many water quality models are flawed either because of their inadequacy to completely simulate the advection component of the pollutant transport, or because of the limited application of the models, due to inaccurate estimation of model parameters. The hybrid cell in series (HCIS) developed by Ghosh et al. (2004) has been able to overcome such difficulties associated with the mixing cell-based models. Thus, the current study focuses on developing an analytical solution for the pollutant transport of the ammonia concentration through the plug flow, the first and second well-mixed cells of the HCIS model. The HCIS model coupled with the first order kinetic equation for ammonia nutrient was developed to simulate the ammonia pollutant concentration in the water column. The ammonia concentration at various points along the river system was assessed by considering the effects of the transformation of ammonia to nitrite, the uptake of ammonia by the algae, the respiration rate of the algae and the input of benthic source to the ammonia concentration in the water column. The proposed model was tested using synthetic data, and the HCIS-NH model simulations for spatial and temporal variation of ammonia pollutant transport were analysed. The simulated results of the HCIS-NH model agreed with the Fickian-based advection-dispersion equation (ADE) for simulating ammonia concentration solved using an explicit finite difference scheme. The HCIS-NH model also showed a good agreement with the observed data from the Umgeni River, except during rainy periods.