Located 360 km north of San Francisco, the Humboldt Bay region contains a wealth of aquatic and terrestrial ecosystems that support a diversity of wildlife species, unique Native American cultures, small communities and towns, and an economy strongly dependent on natural resources. The region is home to approximately 80,000 people. Humboldt Bay is California’s second largest estuary. Over 40% of the eelgrass beds in the state occur in Humboldt Bay, which also serves as habitat for juvenile Dungeness crab, rockfish, salmonids, shorebirds, waterfowl and marine birds. More than 60% of the oysters sold in the state are grown in Humboldt Bay and 60% of the Pacific brant population uses Humboldt Bay for foraging, roosting and staging. In sum, the Humboldt Bay region presents a rich physical, biological and cultural setting.

Humboldt Bay is a drowned river mouth that formed when the rising sea level of the last Ice Age inundated its lower river reaches. The watersheds contributing to the Bay are geologically young with a high rate of tectonic activity. Historically, Humboldt Bay was a large complex of wetland, marsh, and slough habitats, and although the Bay is technically an estuary, in the summer months it functions as a marine lagoonal system. Layered over this physical setting is a legacy in the bay and its contributing watersheds of logging, road building, cattle farming, fishing, lumber and pulp mills, residential development, waterfront development, diking, and dredging.

The Bay and its ecosystems presently experience stresses from both its geological setting and the anthropogenic activities that sustain our local economies. Streams and rivers in the region have been impacted by sediment runoff from surfaced and unsurfaced roads, and three of the four major tributaries to Humboldt Bay are now on the California Clean Water Act Section 303(d) list as impaired due to excessive sediment (NCRWQCB 2001) associated with industrial timber harvest. Many bird and fish populations have declined significantly since the 1970s. Habitat loss and modification are widespread in terrestrial and marine environments. Over 90 species of plants and animals have been accidentally or intentionally introduced into Humboldt Bay (Boyd et al 2002). Threatened and endangered species listed in the Humboldt Bay ecosystem include Coho and Chinook salmon, steelhead, tidewater goby, longfin smelt, marbled murrelet, snowy plover, foothill yellow-legged frogs, Humboldt Bay owl’s clover, and Humboldt Bay wallflower. Pollution has left a legacy of toxins in and adjacent to the Bay, and past and present contamination remains a serious problem.

Humboldt Bay has numerous sloughs and streams entering it including McDaniel Slough (Janes Creek), Butcher Slough (Jolly Giant Creek), Gannon Slough (Campbell, Fickle Hill, Grotzman, Beith, and North Jacoby creeks). Jacoby Creek, Brainard Slough (Washington Gulch and Rocky Gulch), Eureka Slough (Freshwater and Ryan creeks), Elk River, and Salmon Creek. The Humboldt Bay watershed also includes the ancient Headwaters Forest and privately-owned industrial timberlands, agricultural lands mostly used for raising dairy and beef cattle, salmon-bearing streams, as well as many sensitive species.

Along the Bay's wind-swept coast lies an extraordinary dune ecosystem. Sand dunes are formed from sediments washed from the erosive soils of the Franciscan Assemblage by plentiful and intense rainstorms. These sediments are carried to the ocean by the many rivers of the area and are deposited near river mouths. Two of these rivers, the Mad and the Eel, feed sediments into the dunes of the Humboldt Bay region via longshore transport, summer ocean swells, and predominant northwesterly winds. In the winter, large storm waves continue the dune-building cycle by scouring the beach and washing sediments back out to sea. The net effect is the continual building and movement of dunes.

Public lands around the Bay protect and enhance the ecosystem and its wild inhabitants. The Humboldt Bay National Wildlife Refuge protects wetlands, dunes, mudflats, eelgrass beds, and other vital habitats for migratory birds, including the black brandt. The Refuge also includes the Lanphere Dunes and Ma-lei'l Dunes North Units, two of the most pristine remaining dune ecosystems in the Pacific Northwest. The Bureau of Land Management manages the Ma-lei'l Dune South Unit and the Samoa Dunes Recreation Area, also along the Bay.

Nearshore Coast

Variability in the physical ocean environment affects the northern California shelf, and defines the environmental setting. The California Current is an eastern boundary surface current that flows toward the equator and affects the physical oceanographic conditions along the west coast and northern California shelf. Inshore of the California Current, the Davidson current flows toward the equator along the coast in the spring/summer, and seasonally reverses, flowing pole-ward along the coast in the winter. North Pacific waters feeding the California Current are generally low salinity and temperature, with high oxygen and nutrients. The spatial-temporal variability of the California Current affects the continental shelf and the marine biota along the west coast.

North winds blowing in spring and summer result in upwelling of cold,  deep water with low oxygen and high nutrients onto the shelf. The upwelling strength is based on wind strengths and strongly affects productivity and food webs on the shelf. The transition from winter/southwesterly winds to spring/northerly winds that result in upwelling is references as the Spring Transition, which can occur between MArch and June. The earlier in the year that the Spring Transition occurs, the greater the productivity in coastal waters. Variability associated with upwelling is greater across the shelf and can result in hypoxic waters impinging shallow shelf habitats, as observed off large sections of the Oregon shelf in 2002 and 2006.

North Coast Rivers

Rivers remain relatively undeveloped along California's North Coat.  The Klamath, Trinity, Eel, Mad, Smith, and Mattole are the major watersheds that drain the sparsely populated North Coast region. These rivers flow to the Pacific Ocean and account for about 40 percent of the state's total runoff. The Klamath River is California's second greatest river in terms of average annual flow - nearly 13 million acre-feet.
The Smith River is one of the only undammed river systems  in California. The entirety of the Smith River and portions of the Klamath, Trinity, Eel, Smith, Van Duzen, Salmon, and Scott rivers are protected from further dams and diversions under state and federal wild and scenic rivers legislation.  Aside from providing local water supply, these rivers are highly valued for sportfishing, white-water rafting, other forms of river recreation, and for the important salmonid spawning and raring habitat they provide.

Following completion of Lewiston Dam in 1963, up to 90 percent of the Trinity River's flow was diverted east into the Sacramento basin at Claire Engle Lake, part of the Central Valley Project. Consequently, Trinity River salmon and steelhead runs declined by about 90 percent.  In 1981, the Secretary of the Interior ordered diversions reduced by 219,500 acre-feet, and in 1986, Congress authorized the Klamath and Trinity River Basins Fisheries Restoration Act, a 20-year federal and state effort to restore the watershed's fishery.  By early 1992, the Trinity River Hatchery had been modernized and habitat improvement projects were underway to restore native salmon populations. (Laypersons Guide to California Rivers and Streams, Water Education Foundation)

Current efforts to protect and restore North Coast rivers include:

1) Reallocating water rights previously used to support the region's closed pulp mills to environmental uses (i.e. dedicated in-stream flows) versus allowing the water to be re-appropriated as a domestic water supply and potentially transported out of the County, and

2) Removal of four of the six dams on the Klamath River by 2024, opening up 400 river-miles of habitat to salmon, trout, and eels, for the first time in decades in what will be the largest dam removal project in the history of the United States.


The North Coast of California once hosted one of the richest fisheries along the Pacific Coast. Salmon and steelhead are the iconic fisheries of the region, and North Coast rivers - including the Klamath and Eel - once supported enormous populations of Chinook and coho salmon, winter and summer steelhead, and coastal cutthroat trout. A historical review of Eel river salmon and steelhead estimated combined annual runs in the Eel River exceeded one million adult fish in good years (~ 800,000 Chinook salmon, ~100,000 coho salmon, ~150,000 steelhead). Halibut, groundfish, and Dungeness crab rounded out a wealthy commercial fishery. Pacific lamprey and green sturgeon are also recognized as important native species to North Coast rivers.

Our North Coast ecosystems, their salmon and steelhead populations, and other native fish and wildlife populations have been in decline for the past century and a half since the start of Euro-American settlement in the region. Much of the decline may be attributed to loss or degradation of physical and biological conditions in the ecosystem caused by human activities, including commercial and recreational fish harvests and cannery operations, several periods of large-scale timber harvest, land conversion for agricultural activities, water developments and diversions, rural an urban residential development, introduction of non-native species, and a multitude of additional minor factors.

In the late 1990's, due to the decline in the commercial fisheries and poor ecological health of our coastal waterways, state and federal agencies began imposing restrictions and regulations on the North Coast's iconic fishery resources, including entire fisheries bought out with federal funding to reduce impacts. The National Marine Fisheries Service (NMFS) listed Southern Oregon/Northern California Coast (SONCC) coho salmon (1997), California Coastal Chinook Salmon (1999), and Northern California steelhead (2000) as threatened under the federal Endangered Species Act. And the California Fish and Game Commission also listed coho salmon as threatened in 2005. In addition, the United States Environmental Protection Agency (USEPA) has listed North Coast rivers as impaired on the federal Clean Water Act 303(d) list, primarily for excessive sediment and increased water temperatures. The State Board of Forestry imposed new Forest Practice Rules in 2009, restricting many traditional timber harvest practices.

Considerable effort has been made in recent years by resource agencies, private industries, conservation organizations, and other stakeholders - sustained by an infusion of state and federal funding - to promote restoration of salmon habitat, watersheds, and river corridors to protect ecosystem health, bring back our commercial and recreational fisheries, and meet sustainable harvest goals. The vast majority (>90%) of the habitat was diked and leveed over the last 150 years for conversion into land. These changes largely eliminated habitat available to estuarine dependent juvenile salmonids, especially coho salmon whose life cycle exhibits their retention in fresh and brackish water for approximately one full year after emerging as fry. Conservation and restoration actions are underway to protect and restore tidal wetlands, notably the US Fish and Wildlife Service's Humboldt Bay National Wildlife Refuge and restoration of the Elk River estuary.

Emerging Issues

Like many coastal regions, ecosystems in the North Coast and Humboldt Bay face a number of threats from climate change and sea-level rise, including:

  • Nearly 41 miles of dikes on Humboldt Bay are vulnerable to being breached by extreme tides and water elevations, with nearly 7,000 acres currently at risk of being inundated with saltwater. Assuming 1.0 meter of sea level rise, the mean annual maximum tide could:
    • Overtop nearly 58% of existing dikes
    • Inundate approximately 12,000 acres
    • Inundate critical infrastructure including utilities (municipal water lines/pump stations, wastewater lines/lift stations, gas lines, electrical transmission towers, and optical fiber lines) and transportation (Highway 101 and 255 and local roads/streets).
  • Loss of snowpack may reduce summer low flows for local rivers leading to increased stress on fish and other aquatic species.
  • Impacts to fisheries are possible due to shifts in ocean chemistry which lower pH, reducing oyster and clam productivity.
  • Sea level rise may make tidal marshland susceptible to more frequent, longer, and deeper flooding.
  • Higher temperatures and longer dry seasons would increase wildfire risk and impair water quality in local streams and lakes.

(DWR California Climate Science and Data for Water Resources Management, June 2015)

With the highest rate of sea level rise in California - 18.6 inches over the last century - and many populated low-lying areas, the Humboldt Bay region will have to adapt to the challenges of sea level rise sooner than other parts of the state. Highways, sewer treatment plants, contaminated sites, power plants and lines, and drinking water supplies all need to be adapted as we plan for he inevitable and potentially catastrophic changes brought as sea level rises.

Humboldt Bay Ecosystem Quick Facts


275 miles (360 km) north of San Francisco, California
140 miles (225 km) south of Port Orford, Oregon

Watershed: 225 square miles
Sub-basins: Mad River, Janes Creek (incl. McDaniel’s Slough), Jolly Giant Creek (incl Butchers Slough), Cambell and Beith Creeks (incl. Gannon Slough), Jacoby Creek, Washington and Rocky Gulches (incl. Brainard's Slough), Cochran Creek (incl. Fay Slough), Redmond, Freshwater, and Ryan Creeks (incl. Freshwater Slough), Eureka urban creeks, Elk River, and Salmon Creek. Some of the State's most important, viable stocks of Coho salmon, Chinook salmon, and steelhead trout are found in these watershed tributaries.

Land Use:
Timber production – 54%
Open Space and parks – 14%
Urban – 10%
Agriculture – 9%
Rural residence – 7%
Other – 6%

Arcata – 14,000
Eureka – 30,000
Small, rural communities – 33,000 (Fairhaven, Samoa, Manila, Bayside, Freshwater, Kneeland, Cutten, King Salmon, Field’s Landing, Table Bluff)

Humboldt Bay: 25 square miles of surface area at high tide and 8 square miles of surface area at low tide, 102 miles of shoreline, approximately 18,900 acres of open water and mudflats, 1,500 acres of salt marsh, and 23 diked hydrologic sub-units.

4,000 acres of eelgrass
900 acres of salt marsh, reduced from 10,000 acres 130 years ago
60% of Brandt geese in Pacific Flyway population use Humboldt Bay between December
and April, peak spring population of 21,000
More than 110 species of fish
Second only to San Francisco Bay in numbers and diversity of migratory water associated birds wintering in coastal segment of Pacific Flyway of California
Threatened and endangered species include Tidewater Goby, Coho and Chinook Salmon, steelhead, longfin smelt, Foothill yellow-legged frog, Snowy Plover

Littoral Cell: Trinidad Head to Cape Mendocino
40 miles long
Extreme wave climate
Approximately 1 million cubic yards of sand removed annually from harbor entrance