Super typhoon Haiyan struck the Philippines on 8 November 2013, marking one of the strongest typhoons at landfall in recorded history. Extreme storm waves attacked the Pacific coast of Eastern Samar where the violent typhoon first made landfall. Our field survey confirmed that storm overwash heights of 6–14 m above mean sea level were distributed along the southeastern coast and extensive inundation occurred in some coastal villages in spite of natural protection by wide fringing reefs. A wave model based on Boussinesq‐type equations is constructed to simulate wave transformation over shallow fringing reefs and validated against existing laboratory data. Wave propagation and runup on the Eastern Samar coast are then reproduced using offshore boundary conditions based on a wave hindcast. The model results suggest that extreme waves on the shore are characterized as a superposition of the infragravity wave and sea‐swell components. The balance of the two components is strongly affected by the reef width and beach slope through wave breaking, frictional dissipation, reef‐flat resonances, and resonant runup amplification. Therefore, flood characteristics significantly differ from site to site due to a large variation of the two topographic parameters on the hilly coast. Strong coupling of infragravity waves and sea swells produces extreme runup on steep beaches fronted by narrow reefs, whereas the infragravity waves become dominant over wide reefs and they evolve into bores on steep beaches.