Sea level rise increases the risk of storms and other short‐term water‐rise events, because it sets a higher water level such that coastal surges become more likely to overtop protections and cause floods. To protect coastal communities, it is necessary to understand the interaction among multiday and tidal sea level variabilities, coastal infrastructure, and sea level rise. We performed a series of numerical simulations for San Francisco Bay to examine two shoreline scenarios and a series of short‐term and long‐term sea level variations. The two shoreline configurations include the existing topography and a coherent full‐bay containment that follows the existing land boundary with an impermeable wall. The sea level variability consists of a half‐meter perturbation, with duration ranging from 2 days to permanent (i.e., sea level rise). The extent of coastal flooding was found to increase with the duration of the high‐water‐level event. The nonlinear interaction between these intermediate scale events and astronomical tidal forcing only contributes ∼1% of the tidal heights; at the same time, the tides are found to be a dominant factor in establishing the evolution and diffusion of multiday high water events. Establishing containment at existing shorelines can change the tidal height spectrum up to 5%, and the impact of this shoreline structure appears stronger in the low‐frequency range. To interpret the spatial and temporal variability at a wide range of frequencies, Optimal Dynamic Mode Decomposition is introduced to analyze the coastal processes and an inverse method is applied to determine the coefficients of a 1‐D diffusion wave model that quantify the impact of bottom roughness, tidal basin geometry, and shoreline configuration on the high water events