Located on California's rugged north coast, roughly 250 miles north of the Golden Gate Bridge, Humboldt Bay is situated in the Klamath bioregion and is California's second largest natural bay. The Bay's four major watersheds, mostly forested, drain approximately 250 square miles.

The Humboldt Bay watershed contains a rare combination of natural attributes. Within the basin are the ancient Headwaters Forest, privately-owned industrial timberlands, agricultural lands, streams providing salmonid habitat, and a wide variety of wetlands, including the only substantial area of salt marsh between San Francisco Bay and Coos Bay, Oregon. The Humboldt Bay salt marsh community contains two rare species: Humboldt Bay owl's clover (Castilleja ambigua ssp. humboldtiensis) and Point Reyes bird's beak (Cordylanthus maritmus ssp. palustris).

Along the Bay's rugged, wind-swept coast lies an extraordinary dune ecosystem. Sand dunes are formed from sediments washed away from the erosive soils of the Franciscan Assemblage by plentiful and intense north coast rain. These sediments are carried to the ocean by the many rivers of the area, and are deposited at 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. Many of the morphological features of Humboldt Bay sand dunes have been stabilized by native vegetation highly adapted to the dynamic and sometimes harsh environment of the dunes.

Public lands around the Bay protect and enhance the ecosystem and its wild inhabitants. One of these areas is the Humboldt Bay National Wildlife Refuge. The Refuge protects wetlands and bay habitats for migratory birds, especially the black brant. The Refuge also includes the Lanphere Dunes, one of the most pristine remaining dune ecosystems in the Pacific Northwest. Another public-owned jewel is the Arcata Marsh & Wildlife Sanctuary. The Arcata Marsh is an example of the community's involvement in environmental politics, innovative uses of land, and applications of appropriate technology in a small urban community. The marsh has multiple uses including recreation, wildlife habitat, education, and wastewater treatment.