The Willamette River mainstem and its tributaries are listed as water quality impaired (303d list) under the Clean Water Act.  We mapped the spatial distribution of cold water habitats in the upper Willamette River between Albany and Eugene, Oregon.  We used maps of channel and floodplain complexity in the Willamette River in 1850, 1895, 1932, and 1995 to develop a typology of thermal reach types based on associations of thermal characteristics and channel morphology.  Cold water refuges 2 to 8.5˚C colder than the mainstem river were found in alcoves associated with floodplains and in-channel gravel bars.  Spatial characteristics of these features were mapped for twelve 2-km reaches in 2005 and 2006 and related to movement behavior of native salmonids.  We used these data to create dynamic visualizations of ecological relationships and management options.  These were used to identify conservation and restoration actions that would simultaneously protect cold water refuges and provide additional ecosystem services and social benefits.  We are incorporating these approaches in cooperation with the Willamette Partnership and state of Oregon to create WillamEx, a market-based credit trading system to more effective achieve conservation goals and create economic incentives for citizens and communities along the river.