The river flows generally northward through the Coast Ranges west of the Sacramento Valley, emptying into the Pacific Ocean about 10 miles (16 km) downstream from Fortuna and just south of Humboldt Bay.

[4] However, the river basin also supports abundant forests – including some of the world's largest trees in Sequoia sempervirens (Coastal redwood) groves–and, historically, one of California's major salmon and steelhead trout runs.

The river was named after they traded a frying pan to a group of Wiyot fishermen in exchange for a large number of Pacific lampreys, which the explorers mistook for eels.

Although the damming would have relieved pressure on greater California's overburdened water systems, it stirred up decades of controversy, as some of the proposals made little economic sense and would have been detrimental to an ailing salmon run.

Below the South Fork the Eel flows through a wider agricultural valley, past Scotia and Rio Dell, before receiving the Van Duzen River from the east.

At Fortuna, the river turns west across the coastal plain and enters the Pacific via a large estuary in central Humboldt County, about 15 miles (24 km) south of Eureka.

Average flow of the Eel River varies widely due to its location, which places it more or less directly in the path of Pineapple Express-type winter storms.

[4] The lowermost United States Geological Survey (USGS) stream gauge on the Eel where flow volume is measured is at Scotia, where an annual mean of 7,309 cubic feet per second (207.0 m3/s), or 5.3 million acre-feet (6.5 km3) per year, was recorded between 1910 and 2012.

[9] Reduction in flow occurs in part due to deliberate water diversion from the Eel to the Russian River watershed by the Pacific Gas and Electric Company's Potter Valley Project, located to the south in Mendocino County.

The topography creates a general drainage pattern that runs from southeast to northwest, except in the Middle Fork basin and the Eel headwaters, where water flows from east to west.

Beginning several million years ago, tectonic forces shoved the Franciscan assemblage against the North American Plate, pushing up the Coast Ranges.

Terraces were formed due to a combination of the high sediment load of the river system, and the rapid regional rate of geologic uplift (up to 13 feet (4.0 m) per 1000 years, as measured at Scotia Bluffs).

[26] The first westerner to enter the Eel River was Sebastián Vizcaíno, sailing on behalf of Philip III of Spain, seeking a mythical northwest passage described in secret papers as being at the latitude of Cape Mendocino.

The party took months to travel overland by an extremely arduous route from Helena to the Pacific Ocean between November and December 1849, when they are credited with the rediscovery of Humboldt Bay by land.

Although most of the early settlements were made along the coast, some people spread south into the Eel River valley, which offered fertile soils along with other abundant natural resources.

Because the Eel River's twists and turns made it difficult to float the large redwood logs, the timber was cut into smaller rectangular "cants" to make them more manageable.

In 1910 noted American engineer John B. Leonard designed Fernbridge, a 1,320 feet (400 m) all-concrete arched bridge at the site of the earlier Singley's Ferry crossing.

The railroad had the ignominious distinction of being the most expensive (per mile) ever built at the time: it traversed some of the most rugged and unstable topography in California, with 30 tunnels in a 95-mile (153 km) stretch.

Due to huge earth-flows caused by the record rain in 1964, 105 million tons of sediment were carried down the Eel River between December 21–23 as measured at Scotia–more than in the previous eight years combined.

[40] The Eel River watershed lies within the Oregon and Northern California Coastal freshwater ecoregion, which is characterized by temperate coniferous forests consisting largely of Douglas fir and western hemlock.

Sediment deposits indicate the lake may have persisted for as many as several thousand years, which is highly unusual considering the easily eroded rock of the region and the unstable nature of landslide dams in general.

[47] The dam blocked access to steelhead trout spawning grounds in the upper Eel River, causing the summer and winter runs to interbreed.

Originally conceived in the late 1800s and built between 1906 and 1922, the project provides about 159,000 acre-feet (0.196 km3) of additional water for the Russian River system for about 500,000 people in Mendocino and Sonoma Counties.

[62] The Potter Valley Project has been argued by environmental groups to have significant impacts on the salmonid (Chinook and coho salmon and steelhead) populations of the basin.

Occasional large "blocks" of water are also released from Scott Dam to help juvenile salmonids migrate to the sea before temperatures in the lower river become unsuitable for their passage.

The Army Corps of Engineers and Bureau of Reclamation both sought to build dams in the Eel River system which, starting in the 1960s was targeted as a potential new source for the California State Water Project.

[67]: 272  Major dams proposed in the watershed included ones at English Ridge, Bell Springs and Sequoia (Alderpoint) on the main stem, and the infamous Dos Rios on the Middle Fork.

Dos Rios Dam would have flooded 110,000 acres (45,000 ha) of Mendocino County, creating a reservoir of 7.5 million acre-feet (9.3 km3)–the largest in California, at nearly twice the size of Shasta Lake.

By 1969, a strong opposition movement had formed, led by a Round Valley rancher named Richard Wilson, who had studied hydrology at Dartmouth College.

Introduced pikeminnow, in conjunction with the diminished flows due to the Potter Valley Project water diversion, have taken a significant toll on the native fish population below Van Arsdale Dam.