This dataset provides the simulation files and raw output files used in a numerical modeling based study focused of how sea-level rise will impact wave transformation processes and flooding on Fatato Island, Funafuti Atoll. This research utilised a phase-resolving fully nonlinear Boussinesq wave model to simulate wave transformation, runup and overtopping in context of present and future sea level, with different reef response morphologies. Simulations encompass the contemporary tidal range and future sea level rise scenarios up to 1.5 m above present spring high tide. Model outputs are presented in the form of profile and time-series data for water level and velocity data at numerous time-steps and location across. Model outputs and inputs are presented for three different reef response morphologies: 1) static reef that simply drowns with sea-level rise), 2) vertical adjustment of the outer reef flat, and 3) vertical adjustment of the full reef flat. This research does not consider adjustments to reef island morphology.The model used in the research is freely available form http://basilisk.fr/src/green-naghdi.h