Settlement and upstream migration in the Japanese mitten crab (Eriocheir japonica) was investigated in the Seseragi-fishway in the Nagara estuary barrage. Megalopa larvae settled and metamorphosed to crab stage in the upper tidal zone in the Seseragi-fishway. The youngest crabs were nearly two millimeters in carapace width. After attaining a minimum of four millimeters, the crabs began to migrate upstream and reach the freshwater area. Settlement of megalopa larvae occurred mainly in early summer (June) and early winter (December). Their upstream migration to the freshwater area began in July and August. The majority of larvae that settled in winter did not survive and metamorphose to the crab stage due to low water temperatures. Thus, the growth and upstream migration of the Japanese mitten crab seemed to be strongly influenced by water temperature in the estuary. This mode of settlement with two peaks in summer and early winter reflected the temporal pattern of reproduction observed in the sea. In this study, it is clarified that the Seseragi-fishway have a function of settlement and upstream migration for supplement of decreased estuary zone. With respect to engineering works in estuaries such as the Seseragi-fishway, it is recommended that we take into account the processes of settlement and migration of young crabs.