Wildlife and plants During the 19th century, the Upper Klamath Basin's abundance of wetlands and wildlife led explorers to call it a "western
Everglades". The five units of the
Klamath Basin National Wildlife Refuge Complex provide feeding and resting grounds for 3 to 5 million ducks, geese and other waterfowl each year. due to its location adjacent to Cascades, Sierra Nevada and Coast Range ecoregions. Chinook alone numbered up to 800,000, split between fall and spring runs. Before damming, Chinook and steelhead once spawned as far upstream as the Williamson and Sprague Rivers that flow into Upper Klamath Lake. Coho and the anadromous
Pacific lamprey spawned nearly as far upstream as Keno, where a naturally occurring constriction and falls (now the site of Keno Dam) prevented further progress. In California, commercial and tribal fishing in the Klamath were banned in 1934 as salmon runs declined. In 1972, following the controversial arrest of a Yurok subsistence fisherman, the Supreme Court ruled in
Mattz v. Arnptt that the state did not have jurisdiction over tribal fisheries, as Indian reservations were created by federal executive order. Prior to its 2024 removal, Iron Gate Dam was the lowermost dam on the Klamath River and effectively cut off migration and spawning habitat of 675 to 970 km of spawning and rearing habitat in the Upper Klamath Basin.
Environmental issues Gold mining, dam construction, commercial fishing, logging and other human activities heavily damaged anadromous fish runs in the 19th and 20th centuries. The construction of Copco No. 1 Dam in 1918 blocked fish migration to more than of streams in the Upper Klamath Basin. The Trinity River Restoration Program was established in 2000, solidifying plans for permanently increased flows. With restoration efforts, the fall Chinook run recovered to 150,000 per year by the 2010s, with the Klamath, Trinity, Salmon, Scott and Shasta rivers all hosting spawning populations. Spring-run Chinook have continued to decline, averaging less than 2,000 per year in the early 21st century, and are considered at risk of extirpation. The only remaining spawning populations are in the Salmon and South Fork Trinity Rivers. Hybridization with hatchery fish has been a major concern for wild spring-run Chinook in the 21st century. In 2021, the state of California recognized Klamath spring-run Chinook as endangered. Klamath River coho, which spawn only in the fall, have been listed as threatened under the Endangered Species Act since 1997. After the controversial 2001 Klamath Irrigation Project water shut-off, Vice President
Dick Cheney intervened to ensure water supply to farmers. In 2002, the government made water deliveries on the project despite the drought continuing. The lower Klamath River experienced
a mass die-off of at least 34,000 adult Chinook salmon in September 2002, which was attributed to atypically low flows that delayed salmon migration and high water temperatures that allowed massive spread of
ich and
columnaris among the waiting fish. The
House Natural Resources Committee investigated Vice President Cheney for having released extra water to farmers for political gain. In 2006, a federal judge ordered the Klamath Irrigation Project to maintain higher river releases to protect fisheries. During dry seasons, the lower Klamath River also experiences elevated phosphorus and nitrogen levels from irrigation run-off, while toxic
algae blooms result in
eutrophication. These issues were exacerbated by the river's dams, which by slowing flows and exposing more water to solar heating created ideal conditions for algae bloom formation. FERC ruled that as part of the relicensing, PacifiCorp must install fish ladders on the dams. The Link River and Keno Dams, which have fish ladders, would remain. In 2013, the
U.S. Department of the Interior released its final environmental impact statement on the plan. The Klamath Hydroelectric Settlement Agreement was enacted in 2016, outlining the regulatory procedures needed to remove the dams, increase flows for fisheries, maintain irrigation water and power supply, reintroduce salmon to the Upper Klamath Basin, restore habitat impacted by the dams, and provide economic assistance to counties, tribes and residents impacted by dam removal. In 2020, the states of California and Oregon, the Yurok and Karuk Tribes, PacifiCorp, and the newly created Klamath River Renewal Corporation (KRRC) signed a final Memorandum of Agreement to implement the project. This formally requested the federal government to transfer the dams' licenses to KRRC, The first dam to be removed was Copco No. 2 in October 2023. The reservoirs behind Iron Gate, Copco No. 1 and J.C. Boyle dams were drained in January–March 2024, and the dams themselves were demolished by August 2024. This represents the largest dam removal project conducted in the US to date. During and immediately after the removal process, the river experienced a temporary drop in water quality and increase in
turbidity as accumulated sediments behind the dams were flushed out. In March 2024, a large die-off of hatchery Chinook salmon occurred when they were released upstream of Iron Gate Dam. The fish are believed to have succumbed to
gas bubble disease when they passed through the temporary diversion tunnel used to drain Iron Gate reservoir; water flowing through the tunnel had a much greater level of turbulence than expected. Restoration work was already ongoing prior to and during dam removal, and is planned to continue for several years afterward. Restoration is being conducted by Resource Environmental Solutions (RES) under the direction of KRRC. This involves revegetating of newly exposed land in drained reservoirs, stabilizing sediment to prevent erosion, restoring the river's main channel as well as of tributaries On October 17, 2024, the first fall-run Chinook salmon was observed in the Upper Klamath Basin in Oregon. In 2025, the numbers of fish returning to the Upper Klamath Basin jumped, with the
California Department of Fish and Wildlife reporting salmon reoccupying nearly every corner of their historical habitat. For the first time in over 100 years, tagged Chinook were spotted at the confluence of the
Sprague River and
Williamson River, above Upper Klamath Lake. ==Recreation==