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.Plain Language Summary In channel-shoal systems, lateral processes sometimes can be of great significance, for example, influencing salinity and sediment transport, even some biogeochemical matters that influence the water environment. Salinity and sediment transport will have a further effect on navigability, ecology, and so on, for example, sediment deposition issues, which significantly decrease the shipping capacity. Consequently, knowing the accurate information about the flow field and finding a criterion for pronounced lateral processes are important to better understand hydrodynamics and sediment behaviors in channel-shoal systems. Here in this study, we conducted an in situ observation and used numerical simulation to detect and predict a strong lateral flow in the North Passage of the Changjiang Estuary. This shoal-to-channel lateral flow occurred around the end of ebb and caused an intratidal salinity variation at the observation site, close to the deep channel. Therefore, a link between pronounced lateral flows and typical salinity variation can be established. This link can also be found in other estuaries like Hudson River estuary. Findings presented here will help to easily distinguish pronounced lateral flows and better understand the effect of lateral flows.