Recognition of the habitat values of coastal and floodplain wetlands has inspired research and engineering to restore biological functions after widespread species declines. However, the restoration and management of tidal river floodplains requires a more complete understanding of anthropogenic stressors on hydrogeomorphology and ecological processes. River floodplains near the ocean are affected by localized diking and dredging as well as basin-wide stressors such as dams. We evaluated the effects of stressors versus spatial position, both longitudinal and lateral to the mainstem, using physical and biological response variables in river floodplain wetlands. We categorized historical and modern stressors on the hydrogeomorphic regime of the lower Columbia River and estuary, northeast Pacific coast, including basin-scale management and local impacts. Using this categorization, we analyzed 44 attributes using field-collected data from 50 floodplain wetlands. Attributes represent channels, floods, plant communities, and fish communities. Here we show that plant and fish communities are stratified by position along the estuarine–riverine gradient, in contrast to physical habitat characteristics, which are stratified by stressors on hydrogeomorphic regimes and in some cases the lateral distance from the mainstem river on tributaries. Spatial position relative to water-level dynamics and salinity more strongly affect the biota than does stressor history. Stressor effects were greatest on the geomorphology observed in formerly diked, now reconnected wetlands and in wetlands with a history of dredged material placement; historically diked sites had anomalously deep channels with larger cross-sectional areas while sites with dredged material had shallow channels and lower levels of organic carbon in sediment. In wetlands subject only to landscape-scale stressors such as flow alterations by dams, organic carbon levels were higher. These findings provide natural resource managers with opportunities to enhance similarity to natural conditions and better understand future wetland evolution from different baselines of stressor history and river position.