To determine the differences in the ditch environments and mussel composition between floodplains and alluvial fans, two geomorphic types in a Lake Biwa river basin were surveyed. An intrinsic Gaussian conditional autoregressive (CAR) model was applied to assess the relationship between the density of Nodularia douglasiae biwae, the dominant species in the floodplain area, and ditch environment. Relative to the alluvial fan area, ditches in the floodplain area had higher percentages of muddy and sandy substrates, a lower percentage of pebble substrates, greater sediment softness, faster flow velocity, and deeper water depth. N. d. biwae and Pronodularia japanensis were collected in both the floodplain and alluvial fan areas. Lanceolaria grayana and Sinanodonta japonica were captured only in the floodplain area, and Sinanodonta lauta was found only in the alluvial fan area. The differences in the ditch environments between the two geomorphic types and the drought tolerance of the mussel species may explain why the mussel composition differs between the two geomorphic types. The CAR model indicated that N. d. biwae was more abundant in ditches with sandy and soft sediment and with deeper water. It also points to the importance of microhabitat-scale sampling to determine the relationship between unionid density and ditch environment.