Projected sea-level rise will raise coastal water tables, resulting in groundwater hazards that threaten shallow infrastructure and coastal ecosystem resilience. Here we model a range of sea-level rise scenarios to assess the responses of water tables across the diverse topography and climates of the California coast. With 1 m of sea-level rise, areas flooded from below are predicted to expand ~50–130 m inland, and low-lying coastal communities such as those around San Francisco Bay are most at risk. Coastal topography is a controlling factor; long-term rising water tables will intercept low-elevation drainage features, allowing for groundwater discharge that damps the extent of shoaling in ~70% (68.9–82.2%) of California’s coastal water tables. Ignoring these topography-limited responses increases flooded-area forecasts by ~20% and substantially underestimates saltwater intrusion. All scenarios estimate that areas with shallow coastal water tables will shrink as they are inundated by overland flooding or are topographically limited from rising inland.