The idea of water wave control for ease of shipping or energy exploitation has been the subject of extensive research. Yet, most studies are limited to two-dimensional simulations focusing primarily on transformations of small-amplitude linear waves. This paper presents a theoretical and numerical investigation of the hydrodynamic performance of a type of shallow-water waveguides. The concept of an effective refractive index for water waves is proposed through analogy with electromagnetic waves, based on which the wave-controlling mechanism is explained. The precise wave field is revealed using computational fluid dynamics simulations. The numerical model is validated by comparing the numerical predictions with experimental data. Subsequently, the nonlinear wave fields around the waveguide are systematically studied by increasing the incident wave height. The numerical results confirm the significant increase in the wave height above the waveguide platform, as a result of wave refraction and reflection. Such an amplification effect slightly reduces as the nonlinearity of the incident wave increases.