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Abstract Water levels in deltas and estuaries vary on multiple timescales due to coastal, hydrologic, meteorologic, geologic, and anthropogenic factors. These diverse factors increase the uncertainty of, and may bias, relative sea level rise (RSLR) estimates. Here, we evaluate RSLR in San Francisco Bay and the Sacramento-San Joaquin Delta, USA by applying a physics-based, nonlinear regression to 50 tide gauges that determines the spatially varying controls on daily mean water level for water years 2004–2022. Results show that elevated river flow and pumping (99th percentile) raise water level up to 6 m and lower it up to 0.35 m, respectively, and coastal water level variations are attenuated by 30-60% within the Delta. Strong westerly winds raise water level up to 0.17 m, and tidal-fluvial interaction during spring tides and low discharge raises water level up to 0.15 m. Removal of these interfering factors greatly improves RSLR estimates, narrowing 95% confidence intervals by 89–99% and removing bias due to recent drought. Results show that RSLR is spatially heterogeneous, with rates ranging from − 2.8 to 12.9 mm y^-1(95% uncertainties < 1 mm y^-1). RSLR also exceeds coastal SLR of 3.3 mm y^-1in San Francisco at 85% of stations. Thus, RSLR in the Delta is strongly influenced by local vertical land motion and will likely produce significantly different, location-dependent future flood risk trajectories. 

Abstract Subsidence after a subduction zone earthquake can cause major changes in estuarine bathymetry. Here, we quantify the impacts of earthquake‐induced subsidence on hydrodynamics and habitat distributions in a major system, the lower Columbia River Estuary, using a hydrodynamic and habitat model. Model results indicate that coseismic subsidence increases tidal range, with the smallest changes at the coast and a maximum increase of ∼10% in a region of topographic convergence. All modeled scenarios reduce intertidal habitat by 24%–25% and shifts ∼93% of estuarine wetlands to lower‐elevation habitat bands. Incorporating dynamic effects of tidal change from subsidence yields higher estimates of remaining habitat by multiples of 0–3.7, dependent on the habitat type. The persistent tidal change and chronic habitat disturbance after an earthquake poses strong challenges for estuarine management and wetland restoration planning, particularly when coupled with future sea‐level rise effects.