With the global sea level rising, it is imperative to quantify how the dynamics of tidal estuaries and embayments will respond to increased depth and newly inundated perimeter regions. With increased depth comes a decrease in frictional effects in the basin interior and altered tidal amplification. Inundation due to higher sea level also causes an increase in planform area, tidal prism, and frictional effects in the newly inundated areas. To investigate the coupling between ocean forcing, tidal dynamics, and inundation, the authors employ a high-resolution hydrodynamic model of San Francisco Bay, California, comprising two basins with distinct tidal characteristics. Multiple shoreline scenarios are simulated, ranging from a leveed scenario, in which tidal flows are limited to present-day shorelines, to a simulation in which all topography is allowed to flood. Simulating increased mean sea level, while preserving original shorelines, produces additional tidal amplification. However, flooding of adjacent low-lying areas introduces frictional, intertidal regions that serve as energy sinks for the incident tidal wave. Net tidal amplification in most areas is predicted to be lower in the sea level rise scenarios. Tidal dynamics show a shift to a more progressive wave, dissipative environment with perimeter sloughs becoming major energy sinks. The standing wave southern reach of the bay couples more strongly back to the central portion of the bay, in contrast to the progressive wave northern reach of the bay. Generation of the M-4 overtide is also found to vary between scenarios and is a nonnegligible contributor to net changes in high water elevation.