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In this study the sub-tidal and intra-tidal variations of salt fluxes in the upstream section of a shallow estuary (with a water depth of less than 3 m) were investigated. The salt fluxes were estimated based on the cross-sectional average salinity and velocity measured by the fluvial acoustic tomography system (FATS). The results indicate that the magnitude of seaward fluxes is approximately two times greater than that of landward fluxes under normal conditions. The results of short-term observation in the study area indicate that there is a phase lag of the bottom and surface salinities between the regions with the largest and smallest depths. The vertical shear flux with a peak value of −0.7 m2/s during the ebb tide indicated an important contribution to the total salt flux compared with the advective flux. A phase lag occurred between the vertical shear terms in the regions with the largest and smallest depths, which resulted from the correlation between the vertical variations of the salinity and velocity and the existence of transversal velocity circulations.