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The Coastal Inlets Research Program (CIRP) of the U.S. Army Engineer Research and Development Center, Coastal and Hydraulics Laboratory, in collaboration with two universities in Japan, has developed a spectral wave transformation numerical model to address needs of the U.S. Army Corps of Engineers navigation projects. The model is called CMS-Wave and is part of Coastal Modeling System (CMS) developed in the CIRP. The CMS is a suite of coupled models operated in the Surface-water Modeling System (SMS), which is an interactive and comprehensive graphical user interface environment for preparing model input, running models, and viewing and analyzing results. CMS-Wave is designed for accurate and reliable representation of wave processes affecting operation and maintenance of coastal inlet structures in navigation projects as well as in risk and reliability assessment of shipping in inlets and harbors. Important wave processes at coastal inlets are diffraction, refraction, reflection, wave breaking, and dissipation mechanisms, and the wave-current interaction. The effect of locally-generated wind can also be significant during wave propagation at inlets. This report provides information on CMS-Wave theory, numerical implementation, and SMS interface. A set of examples are given to demonstrate the model's applicability for storm-damage assessment, modification to jetties including jetty extensions, jetty breaching, addition of spurs to inlet jetties, and planning and design of nearshore reefs and barrier islands to protect beaches and promote navigation reliability.