Waste stabilization ponds (WSPs) are a common wastewater treatment approach throughout the world. Typically, WSPs are designed with the aid of empirical equations that may not incorporate complex hydrodynamics. Whereas numerical models have been presented as an alternative, they have been limited to two dimensions or lacked validation. In the present study, field monitoring and a high-resolution three-dimensional Delft3D model, incorporating inflows, changing water levels, and wind, are combined to deepen the understanding of WSP hydrodynamics. Observed water levels varied considerably and rapidly, changing by up to 0.5 m within 36 h, and velocities were typically very low (<0.01 m/s), reaching peak speeds of 0.03 m/s during strong winds. Modeled velocities were in good agreement with observations in open water areas, with a root mean square error (RMSE) of 0.003 m/s and an R2 of 0.58. The results indicate that circulation was primarily driven by wind, with a smaller contribution from varying water levels, and circulation patterns were classified into four hydraulic regimes. A dimensionless empirical equation was developed relating the longitudinal current to wind speed, direction, and WSP outflows, providing a tool to predict hydraulics in shallow and enclosed water bodies and representing an important step toward incorporating hydraulic complexity into WSP design.