Since as early as 1869, with the introduction of a federally funded "snag puller" designed to keep the waterway clear, human habitation has affected the ecology of the river basin.
The construction of large federal dams on the Willamette's tributaries between 1941 and 1969 damaged the spawning grounds for spring Chinook salmon and steelhead.
Domestic and industrial waste from the cities built up along the river, "essentially turning the main-stem river into an open sewer by the 1920s."

A 1927 City Club of Portland report labeled the waterway "filthy and ugly", and identified the City of Portland as the worst offender.
The Oregon Anti-Stream Pollution League brought a pollution-abatement measure before the 39th Oregon Legislative Assembly in 1937.
The bill passed, but Governor Charles Martin vetoed it.
The Izaak Walton League and the Oregon affiliate of the National Wildlife Federation countered the governor's veto with a ballot initiative, which passed in November 1938.

Shortly after he was elected in 1966, Governor Tom McCall ordered water quality tests on the Willamette, conducted his own research on the water quality, and became head of the Oregon State Sanitary Authority.
McCall learned that the river was heavily polluted in Portland.
In a television documentary, Pollution in Paradise, he said that "the Willamette River was actually cleaner when the Oregon Sanitary Authority was created in 1938 than it was in 1962."
He then discouraged tourism in the state and made it harder for companies to qualify for a permit to operate near the river.
He also regulated how much those companies could pollute and closed plants that did not meet state pollution standards.

Despite earlier cleanup efforts, state studies in the 1990s identified a wide variety of pollutants in the river bottom, including heavy metals, polychlorinated biphenyls (PCBs), and pesticides along the lower 12 miles (19 km) of the river, in Portland.
 As a result, this section of the river was designated a Superfund site in 2000, involving the U.S. Environmental Protection Agency (EPA) in cleanup of the river bottom.
 The area to be addressed stretches from the Fremont Bridge almost to the Columbia – spanning nearly 11 river miles.
Reducing risk from the pollutants in this stretch will involve removing contaminated sediment from the river bottom and efforts to contain contaminated sediment by placing clean sediment on top (known as "capping").
Pollution has been exacerbated by combined sewer overflows, which the city has greatly reduced through its Big Pipe Project.
Further upstream, the pressing environmental issues have mainly been variations in pH and dissolved oxygen.
The Willamette is nevertheless clean enough to be used by cities such as Corvallis and Wilsonville for drinking water.

Since pollution concerns are primarily along the lower river, the Willamette in general scores relatively high on the Oregon Water Quality Index (OWQI), which is compiled by the Oregon Department of Environmental Quality (DEQ).
The DEQ considers index scores of less than 60 to be very poor; the other categories are 60–79 (poor); 80–84 (fair); 85–89 (good), and 90–100 (excellent).
The Willamette River's water quality is rated excellent near the source, though it gradually declines to fair near the mouth.
Between 1998 and 2007, the average score for the upper Willamette at Springfield (RM 185, RK 298) was 93.
At Salem (RM 84, RK 135), the score was 89, and good scores continued all the way to the Hawthorne Bridge in Portland (RM 13, RK 21) at 85.
Scores were in the "fair" category further downstream; the least favorable reading was at the Swan Island Channel midpoint (RM 0.5, RK 0.8) at 81.
By comparison, sites on the Winchuck River, the Clackamas, and the North Santiam all scored 95, and a site at a pump station on Klamath Strait Drain between Upper Klamath Lake and Lower Klamath Lake recorded the lowest score in Oregon at 19.
Since as early as 1869, with the introduction of a federally funded "snag puller" designed to keep the waterway clear, human habitation has affected the ecology of the river basin. The construction of large federal dams on the Willamette's tributaries between 1941 and 1969 damaged the spawning grounds for spring Chinook salmon and steelhead. Domestic and industrial waste from the cities built up along the river, "essentially turning the main-stem river into an open sewer by the 1920s."
A 1927 City Club of Portland report labeled the waterway "filthy and ugly", and identified the City of Portland as the worst offender. The Oregon Anti-Stream Pollution League brought a pollution-abatement measure before the 39th Oregon Legislative Assembly in 1937. The bill passed, but Governor Charles Martin vetoed it. The Izaak Walton League and the Oregon affiliate of the National Wildlife Federation countered the governor's veto with a ballot initiative, which passed in November 1938.
Shortly after he was elected in 1966, Governor Tom McCall ordered water quality tests on the Willamette, conducted his own research on the water quality, and became head of the Oregon State Sanitary Authority. McCall learned that the river was heavily polluted in Portland. In a television documentary, Pollution in Paradise, he said that "the Willamette River was actually cleaner when the Oregon Sanitary Authority was created in 1938 than it was in 1962." He then discouraged tourism in the state and made it harder for companies to qualify for a permit to operate near the river. He also regulated how much those companies could pollute and closed plants that did not meet state pollution standards.
Despite earlier cleanup efforts, state studies in the 1990s identified a wide variety of pollutants in the river bottom, including heavy metals, polychlorinated biphenyls (PCBs), and pesticides along the lower 12 miles (19 km) of the river, in Portland.  As a result, this section of the river was designated a Superfund site in 2000, involving the U.S. Environmental Protection Agency (EPA) in cleanup of the river bottom.  The area to be addressed stretches from the Fremont Bridge almost to the Columbia – spanning nearly 11 river miles. Reducing risk from the pollutants in this stretch will involve removing contaminated sediment from the river bottom and efforts to contain contaminated sediment by placing clean sediment on top (known as "capping"). Pollution has been exacerbated by combined sewer overflows, which the city has greatly reduced through its Big Pipe Project. Further upstream, the pressing environmental issues have mainly been variations in pH and dissolved oxygen. The Willamette is nevertheless clean enough to be used by cities such as Corvallis and Wilsonville for drinking water.
Since pollution concerns are primarily along the lower river, the Willamette in general scores relatively high on the Oregon Water Quality Index (OWQI), which is compiled by the Oregon Department of Environmental Quality (DEQ). The DEQ considers index scores of less than 60 to be very poor; the other categories are 60–79 (poor); 80–84 (fair); 85–89 (good), and 90–100 (excellent). The Willamette River's water quality is rated excellent near the source, though it gradually declines to fair near the mouth. Between 1998 and 2007, the average score for the upper Willamette at Springfield (RM 185, RK 298) was 93. At Salem (RM 84, RK 135), the score was 89, and good scores continued all the way to the Hawthorne Bridge in Portland (RM 13, RK 21) at 85. Scores were in the "fair" category further downstream; the least favorable reading was at the Swan Island Channel midpoint (RM 0.5, RK 0.8) at 81. By comparison, sites on the Winchuck River, the Clackamas, and the North Santiam all scored 95, and a site at a pump station on Klamath Strait Drain between Upper Klamath Lake and Lower Klamath Lake recorded the lowest score in Oregon at 19.
Willamette River