Floodplains, considered hotspots of biodiversity, are used by a wide range of aquatic and terrestrial species. Over recent decades, floodplains have been modified for cultivation. This contributes to a loss of biodiversity, which has become a key issue in biological conservation in recent years. Paddy agriculture impacts substantially on the biodiversity of floodplains, including freshwater mussels and bitterlings. To model the habitat suitability for Unio douglasiae nipponensis, the itasenpara bitterling host mussel, we used geographical information system tools and field survey methods along with a generalized linear model to examine the environmental conditions of rivers surrounding paddy fields that were subject to water management practices. Water level fluctuations on the floodplains and artificial management of the water level in rivers around the paddy fields both influenced the spatial distribution of U. d. nipponensis, which suggests that traditional rice paddy management practices provide better support for floodplain species than artificially managed water levels.