For the first time, we monitored continuous 2D tidal currents at a shallow tidal junction using the fluvial acoustic tomography (FAT) system during a period of ~ 34.4 days. The horizontal distribution and spatiotemporal variation of the tidal velocities were efficiently estimated by the inverse analysis method, and the reconstructed velocity patterns agreed well with the recorded acoustic Doppler current profiler series data. Additionally, the high frequency observation interval (1-min) used provided us with the opportunity to detect the rapid processes of the transformation of tidal current patterns during flood tide at the junction. These results further demonstrate that FAT is a potent tool for continuously mapping variable 2D tidal currents at shallow tidal junctions. Furthermore, tidal harmonic analyses of the reconstructed tidal currents were performed to clarify the nonlinear spatial evolution processes of the variations in tidal energy, when tides propagated from the estuary to the tidal junction. The sub-tide species (, ) caused significant fortnightly variations in the tidal range along the tidal branches. The variations in the tidal current were dominated by semidiurnal species (D2: , , , ), followed by diurnal species (D1: , , ) and quarter-diurnal species (D4: , ). The / amplitude ratios were higher during low river discharge periods, signifying that the nonlinear tidal distortion varies with river discharge. River-tide interactions strongly affected tidal asymmetry. It is believed that this study provides further understanding of hydrological research in shallow tidal systems.