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Abstract Decreases in shallow-water habitat area (SWHA) in the Lower Columbia River and Estuary (LCRE) have adversely affected salmonid populations. We investigate the causes by hindcasting SWHA from 1928 to 2004, system-wide, based on daily higher high water (HHW) and system hypsometry. Physics-based regression models are used to represent HHW along the system as a function of river inflow, tides, and coastal processes, and hypsometry is used to estimate the associated SWHA. Scenario modeling is employed to attribute SWHA losses to levees, flow regulation, diversion, navigational development, and climate-induced hydrologic change, for subsidence scenarios of up to 2 m, and for 0.5 m fill. For zero subsidence, the system-wide annual-average loss of SWHA is 55 ± 5%, or 51 × 10⁵ ha/year; levees have caused the largest decrease ($${54}_{-14}^{+5}$$ ${54}_{-14}^{+5}$%, or ~ 50 × 10⁵ ha/year). The loss in SWHA due to operation of the hydropower system is small, but spatially and seasonally variable. During the spring freshet critical to juvenile salmonids, the total SWHA loss was$${63}_{-3}^{+2}$$ ${63}_{-3}^{+2}$%, with the hydropower system causing losses of 5–16% (depending on subsidence). Climate change and navigation have caused SWHA losses of$${5}_{-5}^{+16}$$ $5_{-5}^{+16}$% and$${4}_{-6}^{+14}$$ $4_{-6}^{+14}$%, respectively, but with high spatial variability; irrigation impacts have been small. Uncertain subsidence causes most of the uncertainty in estimates; the sum of the individual factors exceeds the total loss, because factors interact. Any factor that reduces mean or peak flows (reservoirs, diversion, and climate change) or alters tides and along-channel slope (navigation) becomes more impactful as assumed historical elevations are increased to account for subsidence, while levees matter less.