This study evaluates the storm surge inundation risk in three anthropogenically infilled estuaries—Xichong, Renshan, and Kaozhouyang—located in the Guangdong–Macao–Hong Kong Great Bay Area, China. By integrating GIS spatial analysis with storm surge modeling, we conducted 204 numerical experiments to simulate storm surge inundation under varying typhoon intensities and astronomical tide conditions. Results revealed that coastal terrain plays a crucial role in influencing storm surge levels and inundation extents. Specifically, the pocket-shaped terrain in the Renshan and Kaozhouyang estuaries amplified storm surges, resulting in higher inundation levels compared to the relatively open terrain of Xichong. Furthermore, anthropogenically reclaimed land in these estuaries appear to be particularly vulnerable to storm-induced inundation. Overall, this study underscores the importance of considering coastline morphology and the anthropogenic modifications of coastal terrain in storm surge risk assessments, offering valuable insights for disaster prevention and mitigation strategies. The use of ArcGIS spatial analysis coupled with storm surge modeling, facilitated by high-resolution DEMs, provides a statistical risk assessment of inundation. However, more complex flooding dynamics models need to be developed, particularly when terrestrial bottom friction information, which is heavily modified by human activities, can be accurately incorporated.