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Pollution

In southeastern Washington, a 50-mile (80 km) stretch of the river passes through the Hanford Site, established in 1943 as part of the Manhattan Project. The site served as a plutonium production complex, with nine nuclear reactors and related facilities along the banks of the river. From 1944 to 1971, pump systems drew cooling water from the river and, after treating this water for use by the reactors, returned it to the river. Before being released back into the river, the used water was held in large tanks known as retention basins for up to six hours. Longer-lived isotopes were not affected by this retention, and several terabecquerels entered the river every day. By 1957, the eight plutonium production reactors at Hanford dumped a daily average of 50,000 curies of radioactive material into the Columbia. These releases were kept secret by the federal government until the release of declassified documents in the late 1980s. Radiation was measured downstream as far west as the Washington and Oregon coasts.

The nuclear reactors were decommissioned at the end of the Cold War, and the Hanford site is the focus of one of the world's largest environmental cleanup, managed by the Department of Energy under the oversight of the Washington Department of Ecology and the Environmental Protection Agency. Nearby aquifers contain an estimated 270 billion US gallons (1 billion m) of groundwater contaminated by high-level nuclear waste that has leaked out of Hanford's underground storage tanks. As of 2008, 1 million US gallons (3,785 m) of highly radioactive waste is traveling through groundwater toward the Columbia River. This waste is expected to reach the river in 12 to 50 years if cleanup does not proceed on schedule.

In addition to concerns about nuclear waste, numerous other pollutants are found in the river. These include chemical pesticides, bacteria, arsenic, dioxins, and polychlorinated biphenyls (PCB).

Studies have also found significant levels of toxins in fish and the waters they inhabit within the basin. Accumulation of toxins in fish threatens the survival of fish species, and human consumption of these fish can lead to health problems. Water quality is also an important factor in the survival of other wildlife and plants that grow in the Columbia River drainage basin. The states, indigenous tribes, and federal government are all engaged in efforts to restore and improve the water, land, and air quality of the Columbia River drainage basin and have committed to work together to accomplish critical ecosystem restoration efforts. Several cleanup efforts are underway, including Superfund projects at Portland Harbor, Hanford, and Lake Roosevelt.

In early 2022, thousands of protestors demonstrated a demand for heightened cleanup efforts within the Hanford Nuclear Site. In June 2022, nearly 200 protestors attended the Hanford Journey Event, an educational tour which allowed those concerned about the Hanford Nuclear Site to learn about proposed cleanup efforts.The Hanford Journey Event was co-sponsored by the Yakama Nation. Davis Washines, a representative from the Yakama Nation Department of Natural Resources, alluded to “ has a lot of meaning to us, to our people. And not just for us, our personal safety, but to this ground, to the water, because they were here before we were”. Congress responded in 2022 by increasing the budget for the Hanford clean-up efforts, after thousands of comments were sent to federal authorities to prevent high-level waste storage at Hanford.

Starting between April to June 2025, the Hanford Nuclear Site is expected to melt radioactive wastes combined with glass flakes at a rate of 21 metric tons per day. The melters being utilized have a lifespan of five years, which requires their replacement in 2030. As of 2023, the Hanford site cleanup project is sixteen years behind schedule. One of the harmful chemicals located in the Hanford site, strontium-90, reached over 2,000 times the standard concentration for drinking water in August 2022.

Timber industry activity further contaminates river water, for example in the increased sediment runoff that results from clearcuts. The Northwest Forest Plan, a piece of federal legislation from 1994, mandated that timber companies consider the environmental impacts of their practices on rivers like the Columbia.

On July 1, 2003, Christopher Swain became the first person to swim the Columbia River's entire length, to raise public awareness about the river's environmental health.

Throughout 2019, a series of wildfires were ongoing in Oregon on indigenous land belonging to the Umpqua Tribe. The Umpqua Tribe lost possession to their former territory in 1853, which is now known as Elliott State Forest. Elliott State Forest has been the subject of many deforestation initiatives over past years. In December 2018, the Umpqua tribe settled in Oregon after purchasing land from the Bureau of Land Management. Michael Rondeau, a descendent of the Umpqua tribe, expressed his contradictory emotions on the acquisition, stating that he felt "sadness that my grandparents and great aunts and uncles and beyond that did not have a day of recognition". On July 14, 2019, in the Milepost 97 wildfires, 25% of the Umpqua's forest territory burned down.

On March 7, 2022, Columbia Riverkeeper, a climate advocacy group, sued Weyerhaeuser, a timber and forest products company, for possible contamination of the Columbia River. Columbia Riverkeeper accused Weyerhaeuser of releasing harmful levels of runoff through their Longview Mill into the Columbia River. Furthermore, Columbia Riverkeeper stated that runoff could result in harmful bacteria growth. As of May 6, 2022, Weyerhaeuser reached a settlement with Columbia Riverkeeper. Weyerhaeuser was determined to contribute US$600,000 for river restoration and proposed potential fines of up to US$5,000 for each subsequent act of pollution between 2023 and 2025.