Population dynamics of the brackish water clam Corbicula japonica were examined in the Kiso estuaries (the Ibi-Nagara Estuary and the Kiso Estuary), central Japan, during the process of larval recruitment. Based on temporal variation in densities (sampling every 2 weeks for planktonic larvae, new settlers, and small individuals, sampling every month for large and commercially important individuals) from May 2001 to April 2004, we conclude that densities of large and of commercially important individuals were determined not by larval supply but by benthic processes. Density-dependent processes were detected between densities of new settlers and recruits. These processes, however, were detected for spring-summer cohorts, but not for autumn-winter cohorts. Spatial distributions of each cohort were almost the same within the Ibi-Nagara Estuary and within the Kiso Estuary, although cohorts were collected mainly in the middle to upper regions of the Ibi-Nagara Estuary but were collected in the upper region of the Kiso Estuary. A shift in an ontogenetic habitat within each cohort was detected in the Ibi-Nagara Estuary but not in the Kiso Estuary: New settlers and small individuals were collected in the upper region while large and commercially important individuals were collected in the middle region. The shift may be explained by tidal migration using byssal threads or by site-specific differences in mortality, although it was not clear why the shift was detected in the Ibi-Nagara Estuary but not in the Kiso Estuary.