Anticipated sea level rise (SLR) threatens intertidal areas and associated ecosystems in estuaries worldwide. There is a need to develop validated modeling tools to assess the impact of SLR on estuarine morphodynamics. This study explores the morphological impact of SLR on a channel-shoal system in San Pablo Bay, a subembayment of San Francisco Bay, California, using a 3-D, process-based modeling approach (Delft3D) including density currents and wave action. The Bay underwent considerable morphologic development in response to variations in fluvial sediment load and discharge associated with a period of hydraulic mining for gold and later damming in the watershed. The availability of a unique 150-year, 30-year sequenced, bathymetric data set provided a rare opportunity for model validation. We investigate a 250-year period of morphodynamic evolution including a 150-year hindcast and a 100-year forecast with different SLR scenarios. The model shows significant skill in hindcasting volumes and patterns of bathymetric development during both net depositional and erosional (1951-onward) periods. Forecasts show that SLR alters the Bay's erosional trend to a depositional trend again. Despite increased sediment trapping rates, the intertidal mudflats drown under all modeled SLR scenarios (42, 84, and 167 cm by end of the 21st century). Our work highlights the potential of using process-based models to assess the morphodynamic impact of SLR. The study also suggests that SLR can greatly increase the loss of intertidal area when landward migration is not possible. Sustainable management strategies are required to safeguard these valuable intertidal habitats.Plain Language Summary Sea level rise is expected to affect coastal areas all around the world including the estuarine environment. In particular, the estuarine intertidal area comprises delicate and valuable ecosystems. Anticipated sea level rise poses questions on the fate of this unique estuarine environment. In this research, we aim to validate a numerical model against observed bed level developments in San Pablo Bay, a subembayment of San Francisco Estuary, to make trustworthy predictions of the estuarine bed including future sea level rise. The model included detailed tidal water movement, wind-wave action, sediment transports, and resulting bed level updates. Our hindcast (1856-1983) showed significant skill in reproducing observed bed level developments. Our forecast shows that sea level rise slowly drowns the intertidal environment. The sea level rise rate is larger than the accretion rate of the mudflats. Mitigation and adaptation strategies are required to ensure the sustainability of the estuarine environment against climate-induced changes.

Intertidal shoals are vital components of estuaries. Tides, waves, and sediment supply shape the profile of estuarine shoals. Ensuring their sustainability requires an understanding of how such systems will react to sea level rise (SLR). In contrast to mudflats, sandy shoals have drawn limited attention in research. Inspired by a channel-shoal system in the Western Scheldt Estuary (Netherlands), this research investigates governing processes of the long-term morphodynamic evolution of intertidal estuarine sandy shoals across different timescales. We apply a high-resolution process-based numerical model (Delft3D) to generate a channel-shoal system in equilibrium and expose the equilibrium profile to variations in wave forcing and SLR. Combined tidal action and wave forcing initiate ridge formation at the seaward shoal edge, which slowly propagates landward until a linear equilibrium profile develops within 200 years. Model simulations in which forcing conditions have been varied to reproduce observations show that the bed is most dynamic near the channel-shoal interface. A decrease/increase in wave forcing causes the formation/erosion of small tidal levees at the shoal edge, which shows good resemblance to observed features. The profile recovers when regular wave forcing applies again. Sandy shoals accrete in response to SLR with a long (decades) bed-level adaptation lag eventually leading to intertidal area loss. This lag depends on the forcing conditions and is lowest near the channel and gradually increases landward. Adding mud makes the shoal more resilient to SLR. Our study suggests that processes near the channel-shoal interface are crucial to understanding the long-term morphodynamic development of sandy shoals.Plain Language Summary Intertidal area is the coastal zone that undergoes a rhythm of wet-dry cycles under the influence of tidal action. Intertidal shoals are vital components of the estuarine environment. They have high ecological value but also help in reducing flood risk by wave attenuation. It is important to understand how these shoals will react to sea level rise in order to plan sustainable management strategies. We developed a high-resolution model to investigate the long-term evolution of an intertidal sandy channel-shoal system. The model describes tidal flow, wave action, and associated sediment transports and generates an intertidal sandy shoal in equilibrium. Changes in equilibrium forcing lead to morphodynamic adaptation. A drop in wave height causes the formation of small-scale tidal levees at the channel-shoal edge, which are also observed in reality. High wind-wave activity causes shoal erosion. Shoals accrete in response to imposing sea level rise, but the accretion rate is smaller than the sea level rise rate leading to the loss of intertidal area and increased inundation. Inclusion of mud makes the shoal more resilient to sea level rise. Our study suggests that processes near the channel-shoal edge are crucial to understanding the long-term morphodynamic evolution of sandy shoals...