Waste stabilization ponds (WSP) are used extensively to provide wastewater treatment throughout the world. A review of the literature indicates that, understanding the hydraulics of waste stabilization ponds is critical to their optimization, the research in this area has been relatively limited and that there is a poor mechanistic understanding of the flow behavior that exists within these systems. This explains why there is no generally acceptable model for predicting its performance. The two-dimensional computational fluid dynamics (CFD) model developed in this study was extensively tested on the waste stabilization pond located in the campus of the University of Nigeria, Nsukka which was used as the field pond and also on a laboratory scale waste stabilization pond obtained from literature. Although the model may be solved by several methods, this research was limited to computational method; numerical solution using finite difference method was used in solving the two-dimensional partial differential equations at steady state conditions. In order to validate the quality of the model, its results were compared with the experimental data from the field and the lab-scale ponds. The results obtained were encouraging, prediction of pond performance with measured values shows that correlation coefficient of 0.82 was obtained, representing an accuracy of 82%. The 2-D model was then used in series of investigative studies such as; effect of single inlet and outlet structures at different positions in the pond, effect of multiple inlet and outlets on the pond’s performance, variation of pond performance with depth, effect of short-circuiting on pond treatment efficiency, effect of baffles on pond performance using laboratory-scale pond data and comparison with tracer studies. In all, the results agree with literature.