1. The vertical and horizontal distribution of unionoid mussels (Pronodularia japanensis) were examined in spring, late summer and winter for different size classes, including juveniles (<20 mm) and large adults (>50 mm), in an agricultural drainage channel in Central Japan. 2. A large number of small-sized juveniles were found at the surface (0-3 cm depth) in spring, whereas approximately half of the adults remained in the deep layer (3-8 cm depth). Most individuals were found in the surface layer irrespective of size classes in summer, and approximately 70% of all individuals descended to the deep layer in winter. 3. Horizontal distribution did not substantially change across seasons and high density patches were consistently found in the areas where substrate appeared to be stable or hydraulically sheltered. Spatial distribution of small juveniles was relatively well predicted by the abundance of adults. 4. The size-frequency distribution was multi-modal in three seasons and estimated numbers of newly recruited juveniles were highly variable in recent years, suggesting that juveniles were rarely found owing to irregular reproduction and/or recruitment not the overlooked habitat preferred by small-sized juveniles. 5. As P. japanensis is characterized by the behaviour of burrowing down to a depth of ∼10 cm, maintaining the processes of sediment deposition appears to be one of the critical criteria for the conservation of mussel habitats in agricultural drainage channel systems, which are commonly lined with smooth concrete materials. [ABSTRACT FROM AUTHOR]