Faced with the need to improve ammonia removal from lagoon wastewater treatment plants (WWTPs) operated in Quebec, Canada, mechanistic modelling has been proposed as a tool for explaining the seasonal nitrification phenomenon and to evaluate optimization and upgrade scenarios. A lagoon model that includes a modified activated sludge biokinetic model and that assumes completely mixed conditions in the water column and sediments has been applied to simulate 3 years of consecutive effluent data for a lagoon from the Drummondville WWTP. Successful prediction of results from this plant indicates that the seasonal nitrification is determined by temperature, dissolved oxygen (DO) concentrations, hydraulic retention time (HRT) of the water column and washout driven by a well-mixed water column. Results also indicate that sediments contribute to the ammonia load in the lagoon effluent, particularly in spring and early summer. Sensitivity analyses performed with the model indicate that the nitrification period could be prolonged by increasing DO concentrations in the lagoon and that bioaugmentation would be particularly effective in spring and early summer. Limitations of the model are discussed, as well as ways to improve the hydraulic model.