We investigated the water-mass structure on the Okinawa Trough and Pacific sides of the southern Ryukyu Island Arc (Yonaguni, Iriomote, and Ishigaki subareas) using the Nd isotope composition (143Nd/144Nd ratios; expressed as εNd values) of benthic foraminiferal tests in surface sediments, which reflect bottom-water composition, along with hydrogen and oxygen isotope compositions (δD and δ18O values, respectively) and physical properties (temperature and salinity) of seawater. The Okinawa Trough side has lower εNd values than the Pacific side due to continental/island material inputs characterized by relatively low εNd values. Moreover, within the Okinawa Trough, other processes control the Nd behavior of seawater and primarily affect the Yonaguni and Iriomote subareas, as follows. (1) Surface and subsurface waters are influenced by Taiwanese river discharge combined with temporospatial variations in oceanographic conditions including Kuroshio Current meandering. (2) Intermediate water is characterized by low εNd values (down to − 8.2), possibly attributable to sediment plumes and turbiditic fluxes. (3) The εNd values of bottom water indicate upwelling and vertical mixing, with composition therefore being similar to those of intermediate water. The εNd profiles are better defined on the Pacific side. High εNd values occur in surface and subsurface (< 300 m depth, potential density < 25.0 kg m−3) waters, and low values (down to − 7.0) occur in subsurface–core-intermediate water (400–600 m depth, 26–27 kg m−3). εNd values increase slightly to − 4.0 below 750 m depth and remain constant down to about 2000 m depth, below which deep water shows a slight decrease in εNd values. Intermediate and bottom/deep waters are distinguished from upper layers by their lower δD and δ18O values.