Developed in this study is a nonlinear Ekman pumping model to be used in simulating the rotating flows with quasi-three-dimensional Navier-Stokes equations. In this model, the Ekman pumping velocity is given from the solution of the Ekman boundary-layer equations for the region adjacent to the bottom wall of the flow domain; the boundary-layer equations are solved in the momentum-integral form. The developed model is then applied to rotating flows in a rectangular container receiving a time-periodic forcing. By comparing our results with the DNS and experimental data we have validated the developed model. We also compared our results with those given from the classical Ekman pumping model. It was found that our model can predict the rotating flows more precisely than the classical linear model.