Over the past 150 years, the Lower Columbia River Estuary controlling depth has approximately doubled, the majority of historical wetlands and floodplain have been reclaimed, numerous infrastructure projects have altered and confined flow pathways, and significant natural and anthropogenic changes to the discharge hydrograph have occurred. To investigate the effect of these changes on tides, river slope, and flood water levels, we construct and validate numerical models that simulate flow over late nineteenth‐century and present‐day bathymetry. The models are validated using archival (1853–1877) and modern tide measurements throughout the Lower Columbia River Estuary and river stage measurements from the tidal river (1876–present). Historical flood plain roughness and levee heights are validated iteratively by requiring simulations to match the observed roll off in the river stage rating curve during floods. Measurements and model results show that environmental change has amplified tidal constituents, with peak change about 60 km from the coast. By contrast, increased depth has reduced river slope for low and moderate river discharge. For rarely observed extreme floods of 30 × 103 m3/s, simulated modern water levels exceed historical in Portland (OR). These observations highlight competing hydrodynamic effects, which are investigated by scaling the St. Venant equations for a simulated 25 × 103‐m3/s flood: While larger modern depth reduces frictional effects and decreases surface slope, reduced floodplain access confines modern flow into channels, increasing velocity, bed stress, and water levels. However, the highly frictional historical floodplain conveyed little flow, limiting the effect of floodplain to storage effects; hence, most simulated historical floods exceed modern levels.