In the Willamette River Basin in northwestern Oregon, stream temperature has been altered by 13 dams operated by the U.S. Army Corps of Engineers (USACE), negatively influencing threatened populations of native salmonids. CE-QUAL-W2, a two-dimensional, hydrodynamic water quality model, has been used to investigate temperature and heat patterns in the Willamette River and the downstream effects of dam operations and other anthropogenic effects on heat and stream temperature. This data release includes the input and output files for six CE-QUAL-W2 models that include Fall Creek downstream of Fall Creek Dam, the Row River downstream of Dorena Dam, the Coast Fork Willamette River downstream of Cottage Grove Dam, the Middle Fork Willamette River downstream of Dexter Dam, the South Fork McKenzie River downstream of Cougar Dam, the McKenzie River downstream of the South Fork McKenzie River confluence, the South Santiam River downstream of Foster Dam, the North Santiam River downstream of Big Cliff Dam, the Santiam River, and the Willamette River as far downstream as Willamette Falls (river mile 26.8) near Oregon City. The models, built by other researchers in the early 2000s to simulate portions of 2001 and 2002, were upgraded to CE-QUAL-W2 version 4.2 with additional USGS modifications to trace heat, water sources, and provide additional outputs. Models are set up to run from late March through October of 2011, 2015, and 2016. Model scenarios documented in this data release were used to investigate the downstream impacts of flow augmentation from various upstream dams.