To examine the importance of the upper estuarine areas of Ariake Bay as a nursery ground for fish, assemblages of larvae and juveniles were compared among various aquatic habitats. The upper estuaries of the bay (the Rokkaku and Hayatsue estuaries) are brackish, highly turbid waters with high tidal velocities, and differ substantially from the Isahaya area, which has been separated from the bay by a man-made dike, to the middle estuary (the Kikuchi estuary). Abundances of larvae and juveniles were higher in the estuaries than in the open bay and Isahaya areas. Abundant species in the upper estuaries were similar to each other, but differed from those of the middle estuary. This was primarily due to larvae and juveniles of fishes that occurred almost entirely in the upper estuaries, such as Acanthogobius hasta, Boleophthalmus pectinirostris, Coilia nasus, Cynoglossus abbreviatus, Nibea albiflora, Odontamblyopus lacepedii, Trachidermus fasciatus and Tridentiger barbatus. These results suggest that the upper estuaries play an important role as nursery grounds for fishes.