[5] Tree stump evidence from the banks near the estuary shows that the area around the mouth of the Eel dropped 11 feet (3.4 m) in the January 26, 1700, Cascadia earthquake.

[7] Game including California mule deer, Roosevelt elk, bear, ducks, geese, brandt, cranes, and other waterfowl were common.

[7] Salmon and other anadromous fish used the Salt River to get to tributaries in the Wildcat Hills where they spawned, and juveniles later matured before swimming downstream to the estuary and returning to the sea.

[9] 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.

[7] By the middle 1870s, 175-foot-long (53 m) steamships sailed 2.5 miles (4.0 km) up the Salt River to the town of Port Kenyon, where the channel was approximately 200 feet (61 m) wide.

"[7] Even with the wide and deep channel, siltation and annual flooding soon resulted in the loss of business and residents from Port Kenyon to Ferndale and Arlynda Corners.

[11] In December 1877, the steamer Continental, which had been making regular trips in and out of Port Kenyon, suffered a steam explosion, wrecked and beached 2 miles (3.2 km) from the entrance of the Eel.

[7][12] After the Continental wrecked, two other steamers, the George Harley and the Alexander Duncan[13] began shipping from Port Kenyon to San Francisco and Eureka.

[12] From 1878 to 1880, the 136-foot-long (41 m) Thomas A. Whitelaw, which was built specifically for Eel River trade, carried 400 tons of cargo with a draft of 13 feet (4.0 m)[12] as well as 46 passengers.

[7] In 1893, the steamer Weeott,[14] with electric lights and substantial passenger amenities, began service carrying butter, eggs, lumber, shakes, shingles, apples, salmon, potatoes, oats, peas, lentils, barley, wool, and other products.

In 1866, Uri Williams, one of the 1852 pioneer settlers, noted that the overall water depth was less than it had been in the earliest days, and he attributed this to the clearing of the country, constant cultivation and stock ranging, all of which had created wash and sediment which was ending up in the rivers.

[7] Commercial fish canning began in 1877 and used the Salt River to ship ten to twelve thousand 1 pound (0.45 kg) cans of salmon a day, prepared by controversial Chinese workers.

[7] Residents from other towns threatened mob action, and the Chinese were protected by law enforcement and moved to an old cookhouse on Indian Island until they could be removed by boat.

[6]: 13  Four years later a United States Coast and Geodetic Survey surveyor pointed out that the dikes and blocked sloughs were silting up and reducing the tidal area of the Salt River delta.

[18] Historical land reclamation activities for agriculture, including tide gates and levees as well as siltation from uphill landslides and erosion, slowly filled in the river over time, reducing the watershed by 42 percent.

[6] Siltation continued; by 1949, the Salt River had become so shallow that "at low tide... parts of it can be waded across by a man with hip boots.

[7] During the 1970s, the California Department of Fish and Game stopped farmers from clearing local channels; willows and brush quickly filled in the riverbed,[6] and caught sediment, stopping nearly all the flow in the lower half of the Salt, leading to flooding, problems with dilution ratios at the Ferndale Water Treatment Plant, and water quality in general.

[6]: 33 Tributary Francis Creek was rebuilt in 2002, and the U.S. Army Corps of Engineers began work on Salt River studies under the aquatic ecosystem restoration program.