As part of the Willamette Basin Geographic Initiative Program, the Environmental Protection Agency (EPA) funded The Nature Conservancy of Oregon to inventory, classify, and map native wetland and riparian plant communities and their threatened biota in the Willamette Valley. Between October 1994 and September 1996, we evaluated 172 wetland and riparian sites throughout the Willamette Valley. A site is a stream or river reach or wetland area that was inventoried at one to many locations. Of these sites, 21 are high-quality remnants important for future protection and restoration efforts. We identified 153 natural communities as occurring in native wetland and riparian habitats, of which 101 are new to the plant community classification of the Oregon Natural Heritage Program. Twenty-six species of rare animals and 23 species of rare plants occur in the Willamette Valley. Thirty-two species of rare plants and animals appear to be directly dependent on wetland and riparian communities in the Willamette Valley, and twenty-two species are dependent on upland communities in the Willamette Valley. Mapping of presettlement vegetation in the Willamette Valley indicates that 456,119 hectares (1,127,071 ac) of wetland and riparian habitat have been lost overall, with 12 communities impacted in particular. As for uplands, 732,432 hectares (1,809,841 ac) of habitat have been lost overall, with 7 natural communities impacted in particular. We recommend local citizen involvement, land purchases and restoration as means of protecting and restoring remnant ecosystems and their biota in the Willamette Valley.