Irrigation ditches are the major habitat of lotic unionid mussels in Japan. To conserve and rebuild irrigation ditches facilitating mussel conservation, suitable physical environments must be clarified. The effect on mussels of paddy fields connected to ditches also needs to be determined. In this study, physical environmental factors that affect the density of unionid mussels were studied in irrigation ditches in Hikone City, Shiga Prefecture, Japan, to examine whether mussel densities were higher around paddy fields. Generalized linear models were used to analyze physical and paddy field environmental variables affecting mussel density. Our results show that sediment type, sediment softness, water depth, and flow velocity of irrigation ditches affect the density of unionid mussels; the effects of each environment factor and their relative importance differed by species. Specifically, the density of Nodularia douglasiae biwae was higher in ditches with sand-gravel sediment, soft sediment, and not adjoining paddy fields. The density of Pronodularia japanensis was higher in ditches with sand-gravel sediment and not adjoining paddy fields. The density of Lanceolaria grayana was higher in ditches with high flow velocity, not adjoining paddy fields, close to Lake Biwa. The density of Sinanodonta japonica was higher in ditches with mud sediment, shallow depth, high flow velocity, and not adjoining paddy fields. The densities of all four species were lower in irrigation ditches that were closely connected to paddy fields, suggesting that paddy drainage water negatively affects the survival of the mussels.