Abstract A dynamic mathematical model was developed to predict the effluent quality of facultative wastewater stabilization ponds. For a sound representation of sediment–water column, water column–atmosphere interactions and stratification due to variations in dissolved oxygen concentrations, a two-dimensional hydraulic model was employed considering dispersed flow and diffusion in horizontal and vertical directions, respectively. Resulting partial differential equation system was solved using finite difference methods and matrix manipulation techniques. The model has been calibrated and evaluated on the basis of collected data from a full-scale facultative stabilization pond in Selcuk, Izmir. Variations of COD, NH 4 -N, PO 4 -P, dissolved oxygen, bacteria and algae concentrations with time and the dimensions of the pond were estimated by using the dynamic model. The model can be used for design of new stabilization ponds and also, for improving the effluent quality of existing ponds.