AbstractA three-dimensional coupled hydrodynamic and water quality model (Deflt3D-WAQ) was applied to evaluate the ability of a computational simulation to reproduce seasonal water quality conditions over a seven-month period in a wastewater stabilization pond located in eastern Ontario, Canada. Trends in effluent nutrient concentrations, pH, and dissolved oxygen were visually reproduced, and root-mean square errors, in comparison with weekly observations (alkalinity, 43 gHCO3 m−3; dissolved oxygen, 4.0 gm−3; NO3, 2.2 gN m−3; PO4, 0.10 gP m−3; NH4, 0.14 gN m−3; pH, 0.65), were consistent with literature values. Three phytoplankton groups (green algae, diatoms, and flagellates) were also simulated. The calibrated model was extended to investigate the effects of changes in pond design on treatment efficiency, including removing the baffle, increasing the pond depth, increasing wind sheltering, and relocating the influent pipe from the pond bottom to the surface. Increasing the pond depth and wind sheltering reduced vertical mixing, sequestering nutrients near the sediments and improving effluent water quality. Removing the baffle had no impact on removal efficiency, and relocating the inlet to the surface reduced pond efficiency. Three-dimensional biogeochemical models thus provide a virtual process-based means for testing pond prototype design.