The resonance of tsunami waves in semi-enclosed bays is paramount in understanding and mitigating the impact of seismic events on coastal communities. Semi-enclosed bays, characterized by their partial enclosure, can amplify the effects of incoming tsunami waves due to resonance behavior, where the natural frequencies of the bay correspond to those of the incoming waves. This resonance phenomenon can significantly increase wave height and inundation levels, posing an increased risk to nearby settlements and infrastructure. Understanding the resonance patterns in these bays is crucial for accurate hazard assessment, early warning systems, and effective disaster preparedness and response strategies. On October 30, 2020, an earthquake occurred between the Turkish Bay of Seferihisar Bay and the Greek island of Samos in the Aegean Sea. Long waves generated by the normal-faulting earthquake caused notable damage to settlements within Seferihisar Bay and the north coast of Samos Island. According to the measurements of the Syros mareograph stations, the wave heights were between 2 and 20 cm and wave periods between 9 and 20 seconds. Based on on-site survey reports conducted after the earthquake, inundation was reported in six settlements within Seferihisar Bay. However, inundation was notably higher in Sığacık and Akarca, reaching 2–3 times higher than in other locations, and the water level reached 2 m high. Given that the variance in inundation levels is attributed to resonance phenomena in Sığacık and Akarca rather than the propagation of tsunami waves, this study focused on conducting wave resonance modeling in Seferihisar Bay. The resonance modeling was performed using the RIDE wave model. Furthermore, the research has been expanded to assess the resonance patterns that might emerge in the event of an alternative earthquake or underwater landslide along the fault line responsible for the seismic event, encompassing wave periods ranging from T = 1–9 minutes and T = 20–30 minutes. Modeling results revealed that on the day of the earthquake, wave heights in Sığacık Marina and Akarca surged by 8.5 times in comparison to the wave height at the epicenter. This increase is notably higher, ranging from 2 to 2.5 times, compared to calculations made for other locations (Demircili, Altınköy, and Tepecik). Consequently, it was concluded that one of the reasons for the heightened effectiveness of inundation in Sığacık and Akarca was attributable to resonance. Moreover, supplementary investigations have indicated that waves with a period of T<9 minutes will pose higher risks for Demircili, Altınköy, Sığacık Marina, and Tepecik compared to the day of the earthquake. By comprehensively studying wave resonance in semi-enclosed bays, researchers and policymakers can better anticipate the potential impact of tsunami events and take measures to protect coastal communities, ultimately increasing resilience and reducing the loss of life and property in vulnerable regions.