Current estimates of flood hazards are often based on the assumption that topography is static. When tectonic and/or anthropogenic processes change the land surface elevation, the spatial patterns of floods might also change. Here, we employ the hydrological and hydraulic modeling to simulate floods in the Kujukuri Plain, Japan, in the years 2004 and 2013, when two severe floods occurred. In between the two floods, land surface elevations were changed by the 2011 Tohoku-Oki earthquake. The effects of land surface elevation changes on inundation areas were quantified by changing input topographies. Our results showed that, without taking into account land surface elevation changes, around 10% of inundation areas were underestimated at the time of flood events in the year 2013. The spatial distribution of inundation locations varied with local topographical features, for example, the areas with backmarsh and valley fill deposits were sensitive to the extent of inundation by land surface elevation changes. The sub-watershed near the coastal shoreline having below-zero meter elevation areas showed that the earthquake-induced land surface elevation changes exacerbated an additional 22% inundation area. This study suggests that the inundation areas will increase in catchments suffering severe settlements, which highlights the necessity of taking into account the spatio-temporal changes of land surface elevations on the assessment of flood hazards.