The Columbia Estuary Ecosystem Restoration Program on the 1468-km²river floodplain was developed over the past decade to provide habitat for threatened and endangered salmon of the Columbia Basin during migration to the Pacific Ocean. Water levels and floodplain habitat availability in the Lower Columbia River and estuary (LCRE) are influenced by tides, river flow, hydropower operations, water withdrawals, dikes, culverts, tide gates, and coastal processes. The removal of barriers to fish passage and macrodetritus export by hydrological reconnection of floodplain habitats along 234 river kilometers is catalyzing changes in physical and biological indicators, which we have measured at >60 reference and >10 restoration sites in research begun in 2004. Key elements of the restoration program are a conceptual model, prioritization, status-and-trends monitoring, database development, adaptive management, and critical uncertainties and effectiveness research. We investigated and quantified ecosystem controlling factors on water surface elevation, channel morphology, microtopography, inundation, large woody debris, and the composition and distribution of tidal estuarine and freshwater plant communities. We used a sum exceedance value metric to describe the influence of spatially varying water level regimes on Populus balsamifera riparian forests, Picea sitchensis swamps, Salix and Cornus sericea wetlands, and brackish and freshwater marshes. Building on these analyses, we recently proposed a system zonation that is based on discrete transitions in the hydrologic regime. The Estuary is comprised of a lower reach with salinity intrusion, the energy minimum, and an upper reach without salinity intrusion. The Tidal River is also comprised of three reaches, in which water levels are increasingly dominated by river flow instead of tides. Our recently completed programmatic evidence-based evaluation of effectiveness used 11 causal criteria to evaluate 10 analyses synthesized under 7 lines of evidence. The evaluation showed that large-scale wetland restoration benefits salmon through cumulative net ecosystem improvement.