Abstract: Ocean Acoustic Tomography (OAT) is an effective technology for the measurement of ocean temperature, sound speed distribution and current field observations in estuaries and bays with complicated hydrological conditions. The frequency of sound plays an important role in the inversion of current and temperature. Both precise positioning and clock accuracy are required for velocity tomography. In this study, a high frequency experiment with two Acoustic Tomography Systems was carried out in the Jiangdong Reservoir of Beixi River in Zhangzhou city. The systems were set up at E and W stations with a distance of 415 m across Jiangdong Reservoir, the mean water depth was 8 m in both location, and transducers were suspended down to 1.5 m depth from surface of river. In order to improve the resolution of travel-time and the inversion accuracy of velocity, 60 kHz sound with a bandwidth of 40 kHz, phase-modulated by the 8th order M sequence, was transmitted every 10 second. The travel-time obtained by systems was well corrected with the river discharge. This experiment suggests that the ocean acoustic tomography, with high frequency sound, can also be regarded as an effective observational method for small-scale coastal estuary areas.