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Accurate prediction of wave overtopping rates is essential for flood risk assessment along coral reef coastlines. This study quantifies the uncertainty sources affecting overtopping rates for vertical seawalls on reef flats, using ensemble simulations with a validated non-hydrostatic SWASH model. By generating extensive random wave sequences, we identify spectral resolution, wave spectral width, and wave groupiness as the dominant controls on the uncertainty. Statistical metrics, including the Coefficient of Variation ((Formula presented.)) and Range Uncertainty Level ((Formula presented.)), demonstrate that overtopping rates exhibit substantial variability under randomized wave conditions, with (Formula presented.) exceeding 40% for low spectral resolutions (50–100 bins), while achieving statistical convergence ((Formula presented.) around 20%) requires at least 700 frequency bins, far surpassing conventional standards. The (Formula presented.), which describes the ratio of extreme to minimal overtopping rates, also decreases markedly as the number of frequency bins increases from 50 to 700. It is found that the overtopping rate follows a normal distribution with 700 frequency bins in wave generation. Simulations further demonstrate that overtopping rates increase by a factor of 2–4 as the JONSWAP spectrum peak enhancement factor ((Formula presented.)) increases from 1 to 7. The wave groupiness factor ((Formula presented.)) emerges as a predictor of overtopping variability, enabling a more efficient experimental design through reduction in groupiness-guided replication. These findings establish practical thresholds for experimental design and highlight the critical role of spectral parameters in hazard assessment. © 2025 by the authors.