The unique ecosystem of estuaries as well as their social and economic usage such as freshwater abstraction are highly dependent on local salinity. Shifts in salt intrusion can have severe consequences. The salinity dynamics are influenced by several natural factors, especially the river discharge and the tides, but also by human activities such as channel deepening. A thorough understanding of salt transport mechanisms and their response to changing conditions is essential for assessing the effects of both natural variability and human activities on salt intrusion. This study applies a detailed salt transport decomposition method to a high-resolution numerical model of the North German Weser River Estuary. The analysis of the cross-channel integrated transport showed an alternating dominance of two up-estuary salt transport mechanisms: the subtidal shear transport, driven by estuarine circulation and the tidally-correlated depth-averaged transport, such as tidal pumping. A novel decomposition method allowing for two-dimensional maps of salt transport is developed and implemented here to understand the local topographical impacts on the salt transport. Our results highlight that the cross-sectionally integrated transport can underestimate the strength of the resolved transport in specific areas, as opposing flows often occur between the channel and adjacent shoals. Furthermore, we investigate a potential future scenario involving channel deepening, finding that it increases subtidal shear transport, particularly in dredged areas. These findings offer new insights into the spatial complexity of salt dynamics and the impact of anthropogenic changes on estuarine environments.