From Lake Ewauna, the Klamath River flows generally southwest, passing the now-drained bed of the once-vast Lower Klamath Lake before descending into the southern Cascade Range below Keno, Oregon. Once through the Oregon Cascades, the river continues into northern California, passing through the Klamath Mountains and along the southern side of the Siskiyou Mountains. It enters the Pacific at Klamath in southwestern Del Norte County, approximately south of Crescent City.
The Klamath River is one of only three rivers that start in, or east of the Cascade Mountain Range in Oregon and reach the Pacific Ocean. The others are the Rogue River and Umpqua River. These three Southern Oregon rivers drain the mountains south of the Willamette Valley. The Willamette River prevents the streams in the northern portion of the state from reaching the Ocean directly.
The river's drainage basin above Upper Klamath Lake is fed primarily by the Williamson River and its tributaries, including the Sprague River, which stretch into south central Oregon west of the Cascades. In California, the Klamath receives the Shasta River from the south approximately south of Yreka, the Scott River from the south in central Siskiyou County, the Salmon River from the east along the border between Siskiyou and Humboldt counties, and the Trinity River from the south at Weitchpec in northern Humboldt County.
Much of the lower course of the river in California is within the Klamath National Forest. The lower course of the river in northern Humboldt passes through the Hoopa Valley Indian Reservation, the Karuk Tribe and the Yurok Indian Reservation.
The 230,000 acre (930 km²) federal Klamath Reclamation Project manipulates the water storage of the basin, which can hold about of spring runoff in Gerber Reservoir, Clear Lake, and Upper Klamath Lake, along with several smaller reservoirs for use irrigation use.
The upper basin water, along with diverted from the Trinity, as well as irrigation projects on the Shasta and Scott river tributaries have all lowered the total river flow supporting out-migrating young salmon in spring and in-migrating adult salmon in the fall.
In 2005, PacifiCorp applied to the federal government to relicense its four hydroelectric dams on the Klamath for up to 50 years. Environmentalists opposed the relicensing, arguing that they should be removed to reopen the upper Klamath to salmon. No decision on the matter has been made to date.
Two years of closed-door negotiations among farmers, Indian tribes, fishermen, conservation groups and government agencies have resulted in an unprecedented—and conditional—agreement to work toward a comprehensive settlement of Klamath water usage. The proposal advocates for the removal of four hydroelectric dams now operating along of the Klamath River in southern Oregon and northern California, as well as resortation projects.
Significant unresolved conditions of the proposed agreement include:
Whitewater rafting and kayaking are popular recreational activities along the upper Klamath River below the J.C. Boyle Dam, and also along the lower Klamath River downstream of the town of Happy Camp.
The first non-natives to explore the Klamath River were Hudson's Bay Company fur trappers working south from Fort Vancouver in the late 1820s. During the winter of 1826 to 1827 Alexander McLeod led the first party to reach the Klamath River. HBC trapping parties continued south into the Sacramento Valley, establishing the Siskiyou Trail.
In the 1960s, a project was proposed that would erect a dam from the mouth of the river, creating a reservoir which would be used to divert water for consumption in Southern California. The dam was to be known as the Ah Pah Dam; it was never built.
The river is considered a prime habitat for Chinook salmon, Coho salmon, steelhead trout, and rainbow trout. Once the third-largest producer of salmon on the West Coast, only a fraction of the river's historic runs remain since the construction of six dams, built between 1908 and 1962. Coho salmon in the Klamath River are listed as threatened under the U.S. Endangered Species Act. In 1963 the largest tributary to the Klamath, the Trinity River, was virtually removed from the Klamath drainage with the completion of the Lewiston and Trinity dams, diverting 90 percent of the Trinity's flow to the Sacramento Valley. Only per second was left to flow to the Klamath. In 1991, a minimum Trinty flow of 340,000 acre feet was established, a minimum annual flow of about 470 cfs.
The possible removal of the dams has been a controversial issue in the region in recent years. Despite intense lobbying by local Native American tribes, conservationists, and fishermen, the 2004 renewal application by PacifiCorp for another 50-year federal operating licence for the dams did not include any provisions for allowing salmon to return to more than of former habitat above the dams. In January 2007, however, the federal government ruled that PacifiCorp must equip four dams with fish ladders, a modification which would cost potentially more than $300 million. PacifiCorp has offered $300 million to upgrade the JC Boyle fish ladder and proposed trucking fish around the Copco #1 and Iron Gate dams, after having had been denied a licence to build a power generator in Utah. "The fact that the Klamath project is an emissions-free, renewable resource will make it more valuable to our customers in the future and reduce our overall carbon footprint," PacifiCorp President Fehrman said in a statement.
A separate controversy surrounds the use of water in the Upper Klamath Basin for irrigated agriculture, which was temporarily halted in 2001 to protect endangered salmon and lake fish during a severe drought. The federal government, under Interior Secretary Gale Norton, reversed this decision in 2002, and provided full water deliveries to irrigators as the drought continued despite the fact that Klamath area tribes have treaty rights that predate the settlement of the farmers. Norton argued for a "free market" approach by allowing farmers to sell the water to the Native Americans downstream.
According to biologists from the state of California and the U.S. Fish and Wildlife Service, the atypical low flow in the river along with high fish return numbers and high water temperatures allowed for a gill rot disease to kill at least 33,000 salmon in September 2002, which died before they could reproduce. The kill was downstream of the Trinity inflow, and the salmon of the Trinity were impacted to a greater degree than the Klamath as the Trinity run was at its peak. The report does mention that the official fish kill estimate of 34,056 is probably quite low and could be only half of the actual loss.
Klamath flows as measured at the river gauge in Keno show a low flow of per second in September 1908 (before irrigation began). During the 2002 fish kill, flows of per second were recorded. During September of the 2001 irrigation shut off, an average of per second was recorded.