Eureka's Pacific coastal location on Humboldt Bay adjacent to abundant Redwood forests provided a rich environment for the birth of this 19th century seaport town. Beginning more than 150 years ago, miners, loggers, and fishermen began making their mark in this pristine wilderness of the California North Coast. Before that time the area was already occupied by small groups of indigenous peoples.

The Wiyot people lived in the area now known as Eureka for thousands of years prior to European arrival. They are the farthest-southwest people whose language has Algonquian roots. Their traditional coastal homeland ranged from the lower Mad River through Humboldt Bay and south along the lower basin of the Eel River. The Wiyot are particularly known for their basketry and fishery management. An extensive collection of highly evolved basketry of the areas indigenous groups exists in the Clarke Historical Museum in Old Town Eureka.

European exploration of the coast of what would become northern California, beginning as early as 1579, repeatedly missed definitively locating Humboldt Bay for nearly three hundred years. This was due to a combination of geographic features, often aided by weather conditions, which concealed the narrow entrance from view. Despite a well-documented 1806 sighting by Russian explorers, the bay was not definitively known by Europeans until an 1849 overland exploration provided a reliable accounting of the exact location of what is the second largest bay in California. The timing of this discovery would lead to the May 13, 1850 founding of the settlement of Eureka on its shore by the Union and Mendocino Exploring (development) companies.

Secondarily to the California Gold Rush in the Sierras, prospectors discovered gold in the nearby Trinity region (along the Trinity, Klamath, and Salmon Rivers). Because miners needed a convenient alternate to the tedious overland route from Sacramento, schooners and other vessels soon arrived on recently discovered Humboldt Bay. Though the ideal location on Humboldt Bay adjacent to naturally deeper shipping channels ultimately guaranteed Eureka's development as the primary city on the bay, Arcata's proximity to developing supply lines to inland gold mines ensured supremacy over Eureka through 1856. "Eureka" is a Greek word meaning "I have found it!" This exuberant statement of successful (or hopeful) California Gold Rush miners is also the official Motto of the State of California.

The first Europeans venturing into Humboldt Bay encountered the indigenous Wiyot. Records of early forays into the bay reported that the violence of the local indigenous people made it nearly impossible for landing parties to survey the area. After 1850, Europeans ultimately overwhelmed the Wiyot, whose maximum population before the Europeans was in the hundreds in the area of what would become the county's primary city. But in almost every case, settlers ultimately cut off access to ancestral sources of food in addition to the outright taking of the land despite efforts of some US Government and military officials to assist the native peoples or at least maintain peace. A tragic slaughter took place on Indian Island int the spring of 1860, committed by a group of locals, primarily Eureka businessmen. The chronicle of the behavior of European settlers toward the indigenous cultures locally and throughout America is presented in detail in the Fort Humboldt State Historic Park museum, on the southern edge of the city.

The soon to be center of commerce opened its first post office in 1853 just as the town began to carve its grid pattern into the edge of a forest it would ultimately consume to feed the building of San Francisco and beyond. Many of the first immigrants who arrived as prospectors were also lumbermen, and the vast potential for industry on the bay was soon realized, especially as many hopeful miners realized the difficulty and infrequency of striking it rich in the mines. By 1854, after only four years since the founding, seven of nine mills processing timber into marketable lumber on Humboldt Bay were within Eureka. A year later 140 lumber schooners operated in Humboldt Bay, supplying lumber to other booming cities along the Pacific coast. Rapid growth of the lumber industry, depletion of forests located in close proximity to Humboldt Bay and technological advances led to the development of dozens of local, narrow gauge railroads to move the giant trees to dozens of lumber mills on Humboldt Bay.

A bustling commercial district and ornate Victorians rose in proximity to the waterfront, reflecting the great prosperity experienced during this era. Hundreds of these Victorian homes remain today, of which many are totally restored and a few have always remained in their original elegance and splendor. The representation of these homes in Eureka grouped with those in nearby Arcata and the Victorian village of Ferndale are of considerable importance to the overall development of Victorian architecture built in the nation. The magnificent Carson Mansion on 2nd and M Streets, is perhaps the most spectacular Victorian in the nation. The home was built between 1884-1886 by renowned 19th Century architects Newsom and Newsom for lumber baron William M. Carson. This project was designed to keep mill workers and expert craftsman busy during a slow period in the industry. Old Town Eureka, the original downtown center of this busy city in the 19th Century, has been restored and has become a lively arts center. The Old Town area has been declared an Historic District by the National Register of Historic Places. This nexus of culture behind the redwood curtain still contains much of its Victorian architecture, which, if not maintained as homes, have been transformed into scores of unique lodgings, restaurants, and small shops featuring a burgeoning cottage industry of hand-made creations from glass ware to wood burning stoves and a large variety of art created locally.

Eureka's founding and livelihood was and remains linked to Humboldt Bay, the Pacific Ocean, and related industries, especially fishing. Salmon fisheries sprang up along the Eel River as early as 1851, and within seven years, 2,000 barrels of cured fish and 50,000 pounds of smoked salmon were processed and shipped out of Humboldt Bay annually, primarily from processing plants on Eureka's waterfront, which exist to this day. By 1858 the first of many ships built in Eureka was launched, beginning an industry that spanned scores of years. The bay is also the site of the west coast's largest Oyster farming operations, which began its commercial status in the nineteenth century. The Bay remains the home port to more than 200 fishing boats in two modern marinas which can berth at least 400 boats within the city limits of Eureka.

In addition to ethnic conflict with the native and Wiyot peoples, some Eurekans joined the statewide response to the increasing Chinese presence in the 1880s. Californians led the nation in the xenophobic response to the perceived large numbers of Chinese immigrants, which ultimately led to the US Chinese Exclusion Act of 1882 (forms of this law remained in the US Code until 1943). Economic downturns and resulting competition for jobs especially led some citizens of European descent to commit sometimes violent racist actions, especially on the Pacific coast. In February 1885, the racial tension in Eureka broke when a member of two rival Chinese gangs accidentally shot and killed a Eureka City Councilman in the crossfire between the two opposing tongs (gangs). This led to the convening of an angry mob of 600 Eurekans and resulted in the forcible, permanent expulsion of all 480 Chinese residents of Eureka's Chinatown (a one block area). The expelled Chinese unsuccessfully attempted to sue for damages. In the U.S. Circuit Court case Wing Hing v. Eureka, the court noted that the Chinese owned no land and held that their other property was worthless. A citizen's committee then drafted an unofficial law decreeing:

1) That all Chinamen be expelled from the city and that none be allowed to return.2) That a committee be appointed to act for one year, whose duty shall be to warn all Chinamen who may attempt to come to this place to live, and to use all reasonable means to prevent their remaining. If the warning is disregarded, to call mass meetings of citizens to whom the case will be referred for proper action.3) That a notice be issued to all property owners through the daily papers, requesting them not to lease or rent property to Chinese.