Long-term variations of streamflow in a tidal channel were measured using a Fluvial Acoustic Tomography (FAT) system through one transmission path. FAT is an innovative acoustic technology that utilizes the time-of-travel method to determine velocity between two points from multiple ray paths that traverse the entire cross-section of stream. Due to high spatial variability of flow distribution stationary ADCP measurements were not likely to yield true section-averaged flow velocity and moving-boat ADCP method was therefore used to provide reference data. As such, two short-term moving boat ADCP campaigns were carried out by the authors. In the first campaign, a couple of acoustic stations were added to the FAT system in order to resolve flow angularity in addition to the mean velocity. Comparing the FAT results with corresponding ADCP section-averaged flow direction and velocity indicated remarkable consistency. Second campaign was designed to capture the influence of salt wedge intrusion on the sound propagation pattern. It was found that FAT velocity measurements bias high if acoustic stations lay inside the cooler freshwater layer. Ray-tracing hindcasts suggest that installing acoustic stations inside the salt wedge may significantly improve function of output of the system. Comparing salinities evaluated from long-term FAT travel time records with nodal salinity measurements provided by conductivity-temperature sensors reveals the potential ability of FAT in measuring salt flux.