Structures in maritime waterways are subject to loads from ship waves. Initially designed for wind-wave loads, they now show serious damages. In order to provide the relevant hydraulic design parameters for protective rubble mound structures in maritime waterways, the multi-dimensional ensemble empirical mode decomposition (MEEMD) is applied for the time-frequency analysis of ship-induced waves in narrow waterways. By MEEMD, the long-period primary and short-period secondary waves will be separated and their propagation angle determined. Actual results from the project and examples for the application of MEEMD as time-frequency decomposition and analysis for 3D ship-wave fields will be presented.