Adopting a comprehensive, basin-wide method for preventing flood disasters would be effective to deflect the climate-change-induced intensified water-related disasters. This study considers the land use and settlement patterns based on microtopography and flood risks. The influence of the microtopography and alluvial lowland characteristics on the location and development of residential areas in the Kuji River basin, Japan, is a fundamental aspect of historical knowledge. Investigating the relation between the microtopography and the location of antiquities shows that most of the relics dating to or before the third century were situated in the terraces near the lowlands. The development of lowlands near the mainstream of the Kuji River began around the third century. Furthermore, the relation between the microtopography and development of residential areas is investigated using building density as the development indicator. The results confirm the increase in building density in the alluvial surface, proving a history of flood damage and delayed development compared to other regions. This investigation reveals land development in areas, including the former river bed on the mouth of the Kuji River and the flood plain on the margins of the Hitachiota urban distinct, with no confirmed inhabitation before modern times because of elevated flooding risk.