Lateral flow significantly contributes to the near-bottom mass transport of salinity in a channel-shoal system. In this study, an integrated tripod system was deployed in the transition zone of a channel-shoal system of the Changjiang Estuary (CE), China, to observe the near-bottom physics with high temporal/spatial resolution, particularly focusing on the lateral-flow-induced mass transport. These in situ observations revealed a small-scale salinity fluctuation around low water slack during moderate and spring tidal conditions. A simultaneous strong lateral current was also observed, which was responsible for this small-scale fluctuation. A high-resolution unstructured-grid Finite-Volume Community Ocean Model has been applied for the CE to better understand the mechanism of this lateral flow and its impact on salinity transport. The model results indicate that a significant southward near-bed shoal-to-channel current is generated by the salinity-driven baroclinic pressure gradient. This lateral current affects the salinity transport pattern and the residual current in the cross-channel direction. Cross-channel residual current shows a two-layer structure in the vertical, especially in the intermediate tide when the lateral flow notably occurred. Both observation and model results indicate that near-bottom residual transport of water moved consistently southward (shoal to channel). Mechanisms for this intratidal salinity variation and its implications can be extended to other estuaries with similar channel-shoal features.@en