We developed the HyCReWW metamodel to predict wave run-up under a wide range of coral reef morphometric and offshore forcing characteristics. Due to the complexity and high dimensionality of the problem, we assumed an idealized one-dimensional reef profile, characterized by seven primary parameters. XBeach Non-Hydrostatic was chosen to create the synthetic dataset and Radial Basis Functions implemented in Matlab were chosen for interpolation. Results demonstrate the applicability of the metamodel to obtain fast and accurate results of wave run-up for a large range of intrinsic coral reef morphologic and extrinsic hydrodynamic forcing parameters, offering a useful tool for risk management and early warning systems. These data accompany the following publication: Rueda, A., Cagigal, L., Pearson, S., Antolinez J.A.A., Storlazzi, C., van Dongeren, A., Camus, P., Mendez, F.J., 2019, HyCReWW: A hybrid coral reef waves and water level metamodel: Computers & Geosciences, https://doi.org/10.1016/j.cageo.2019.03.004.