The EPA Environmental Monitoring and Assessment Program began sampling the Upper Mississippi, Missouri and Ohio Rivers in 2004 and 2005 as part of an integrated assessment of ecological condition. These Great Rivers of the mid-North American continent are important human recreational destinations and transportation corridors, and represent significant wildlife habitat.  Riparian and instream habitat measures are needed to fully characterize these waterbodies and diagnose causes of degradation.  Principal Components Analysis (PCA) was used to identify influential habitat variables. On the Mississippi River, PCA axis 1 divided reaches with forested riparian zones from highly revetted sites with little riparian vegetation. Axis 2 separated sites along a gradient of large woody debris and other fish cover.  PCA axes 1 and 2 accounted for 43 percent of the variation between sites on the Missouri River, with axis 1 again dividing well-vegetated from unvegetated riparian zones and axis 2 sorting reaches by degree of bank revetment, and by littoral slope and depth.  Sites on the Ohio river were also separated by extent riparian vegetation, as well as ample in-river woody debris vs. heavily agricultural areas.  Results will be integrated into indices that express macroinvertebrate and fish habitat requirements and used to identify human-induced stressors.