Bathymetric measurements show that a deep, subtidal channel in San Pablo Bay, California, has consistently narrowed during the past 150 years. This raises general questions on the seasonal and intertidal morphodynamic processes acting at the subtidal channel-shoal interface. The current work addresses these questions using a process-based morphodynamic model (Delft3D). Model results reveal considerable morphodynamic activity during a tidal cycle. Deposition on the channel margin is largest during flooding of the shoals. Erosion rates (mainly occuring during ebb) remain relatively small, so that net accretion occurs on much of the channel margin. A remarkable finding is that locally generated wind waves are responsible for shoal extension and depositional channel narrowing. High suspended sediment concentration (SSC) in the channel is a critical factor. Apart from sediment supply during high river flow, wind waves suspending sediment on the shoals cause high SSC levels in the channel at ebb. Sensitivity analysis shows that wind direction even determines the location of channel margin accretion. Fluvial sediment supply is another cause of high SSC in the channel. Density currents, 3-D circulation flows, sea level rise, or varied sediment characteristics only have a limited effect on the erosion and sedimentation patterns. A 30 year forecast shows that deeper shoals and decreasing fluvial sediment supply lower SSC levels in the channel, limit channel margin accretion, and even lead to net channel margin erosion in some areas. Channel shape thus remains subject to dynamic processes related to local variations in sediment supply, albeit to a more limited extent than in earlier decades.