To predict the effects of dredging operations in the Western Scheldt estuary, insight into the morphological behaviour of its channels is needed. The estuary features two large main channels that meander alongside each other and that are linked by smaller connecting channels. These connecting channels originate from water level differences between the two main channels. Three hydrodynamic mechanisms are investigated that are responsible for generating such water level differences: (1) differences in tidal wave propagation along two neighbouring main channels, (2) centrifugal forces, and (3) Coriolis forces. The magnitude of the three mechanisms is analytically assessed based on channel geometry, which is derived from historical depth charts. The analysis demonstrates a large temporal variability of the water level differences due to tidal wave propagation, mainly as a function of changes in the depth ratio between the two main channels. Conversely, both the centrifugal effect and the Coriolis effect are relatively constant over time. The temporal evolution of the connecting channels can therefore primarily be attributed to the wave propagation mechanism. A correlation analysis reveals a linear relationship between connecting channel dimensions and the net water level differences produced by the three processes. The relationship suggests that dredging operations may significantly influence the evolution of connecting channels by changing the depth ratio between the two main channels. The proposed future deepening of the navigation channel is therefore expected to induce a decline in the size, or even a total disappearance, of connecting channels in some parts of the estuary.