Abstract: Two water profiles are selected from the northern part of the Okinawa Trough and the elements, such as carbon, chlorine, and boron isotopes and ion concentrations analyzed for investigation of the control factors of the ion and isotope compositions, water source, and modern water exchange process of the water profiles. It is seen that the properties of surface water, subsurface water, and intermediate water in the water profiles are obviously different. The ion concentrations of K⁺, Ca²⁺, and SO₄²⁻ in the ST2 profile increase with water depth, and the vertical changes of δ¹³C, δ¹¹B, and δ³⁷Cl fluctuate substantially. The vertical changing pattern of ion concentrations, and isotopes along the profile ST19 is opposite to the profile ST2. The surface water (0～100 m) and subsurface water (100～300 m) of the profiles ST2 and ST19 are mainly coming from KSW（Kuroshio Surface Water）and KTW（Kuroshio Tropical Water）, affected by CDW（Changjiang Diluted Water）/shelf water, whereas the composition of the intermediate water (300～1000 m) is similar to that of NPIW（North Pacific Intermediate Water) and SCSIW（South China Sea Intermediate Water）. There are obvious north-south differences in water composition between the two profiles, owing to the differences in locality, CDW/shelf water transmission path, local upwelling caused by regional topography and the proportions of NPIW and SCSIW in the water profiles.