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.