Human schistosomiasis is a serious parasitic disease caused by infection with Schistosoma japonicum. In order to establish monitoring sites in the S. japonicum endemic area in the Obitsu River basin in Chiba Prefecture, Japan, we investigated the habitat of the intermediate snail host, Oncomelania hupensis nosophora using geographic information systems (GIS). A series of thematic maps of soil types, land-use, and past wetlands were compared to the distributions of patients and O. h. nosophora habitats to identify environmental conditions associated with high risk of the disease. In addition, we divided the period from the 1600s to the present into four sub-periods to estimate how the habitat of O. h. nosophora has changed. Our study identified the present risk areas in the Obitsu River basin that should be monitored consecutively, taking into account future global environmental changes that may have the potential to promote re-emergence of the disease.