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The protective capability of fringing reefs against tsunami hazards has been reported in numerous post-disaster surveys. It is believed that global warming is changing the water level over the reef flat and reef surface roughness by sea-level rise and coral bleaching. For a better understanding of the influence of climate change on tsunami hazards over fringing reefs, this study utilized a shock-capturing Boussinesq wave model, FUNWAVE-TVD, to simulate the tsunami-like solitary wave propagation and run-up over fringing reefs. Calibrated and validated by the newly obtained experimental data, the present model with shock-capturing scheme, in which only the ratio of wave height to water depth is used to trigger wave breaking, shows reasonable prediction of solitary wave transformation and run-up height over sharply varying reef bathymetry. Numerical experiments were then carried out to investigate the effects of sea-level rise and degrading of the reef surface roughness on the solitary wave inundation distance and fluid force distribution in the inundation zone. Numerical results clearly demonstrate how tsunami hazards change within the inundation zone in response to higher water levels and lower reef roughness and suggest climate change, especially sea-level rise, will significantly increase tsunami hazards in the low-lying areas of the reef-lined coasts. Presented results are discussed for the effects of sea-level rise and coral bleaching on the solitary wave process and implications to further improve the resilience under the threat of climate change.