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 are legacy effects in the bay and its contributing watersheds from 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.