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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.