Tracer studies performed in two aerated facultative lagoons indicate some bypass and an overall hydraulic regime close to completely-mixed. Results were used to calibrate a hydraulic model based on the tanks-in-series approach. The hydraulic model was combined with a simple "death-regeneration" biokinetic model to simulate seasonal nitrification as observed over a three year period. Modifications were made to the hydraulic model to represent the effect of baffle installations to 1) eliminate bypass and 2) impose a plug-flow regime. Simulation results indicate there is some gain to eliminating bypass but that imposing a plug-flow regime would increase biomass washout rates and hinder nitrification.