Non-zonal hybrid Reynolds-averaged Navier-Stokes (RANS) and large-eddy simulation (LES) are commonly used for predicting unsteady flows in pumps. However, these hybrid methods often face challenges in the transition between the RANS and LES regions, known as the “grey area” problem. In this study, a pure LES approach, coupled with wall modeling to eliminate this issue, was employed to simulate unsteady flow in a water-jet pump (WJP). A grid generation method, based on turbulent length scales derived from a precursor RANS calculation, was developed to address the complexities of grid design in wall-modeled large-eddy simulations (WMLESs) for complex geometries. Initially, the accuracy of the wall model was validated in the fully developed channel flow. The grid generation method and the accuracy of WMLES in predicting unsteady fluctuations were validated using the flow over a flat strut with an asymmetrically beveled trailing edge. The predicted fluctuation spectra at monitored points showed strong agreement with experimental data. The grid generation method was then applied to WMLES of flow in a WJP, where experimental measurements of the pump head rise and torque were accurately calculated by the numerical simulations. The results from three different grid resolutions were compared with experimental data, revealing significant changes in the predicted mean and transient fields as the grid was refined. The grid based on the turbulent length scales reproduced both the hydrodynamics and transient vortices with high accuracy and detailed resolution. These comparisons demonstrated that pure LES with wall modeling effectively predicts the mean and fluctuating characteristics of high Reynolds number flows with reasonable computational cost. The turbulent length scale-based WMLES enhance the fidelity of computational tools for simulating pump flows.