Data on river discharge is an important hydrological factor for river and coastal planning and management, control of water resources, and environment conservation. However, it is difficult to measure crosssectional mean water velocity in complex flows such as tidal estuaries or during extreme hydrologic events such as floods. In this study, water discharge in a shallow tidal channel had been continuously measured using a new fluvial acoustic tomography system. In addition to measuring water discharge, mean water temperature and salinity were deduced from processing the sound speed data collected by the fluvial acoustic tomography system. The system was installed at a shallow tidal channel where water depth and salinity change significantly. It was found that the acoustic tomography system could successfully measure the cross-sectional mean velocity over a long duration.