Humboldt Bay National Wildlife Refuge is located on Humboldt Bay, on the coast of northwestern California. The refuge exists primarily to protect and enhance wetland habitats for migratory water birds using the bay area, including tens of thousands of shorebirds, ducks, geese, swans, and black brant.

During the spring, the bay's eelgrass beds are a key staging area for brant prior to their return to Arctic nesting grounds; and the refuge grasslands provide important habitat for thousands of Aleutian Canada geese. Like many of the refuges in the system, this one was established to preserve habitats recognized to be instrumental to the perpetual survival of migratory birds and other wildlife.

Humboldt Bay NWR, along with other public and private lands around Humboldt Bay, helps this area remain one of the key points for the millions of migratory birds that rely on the Pacific Flyway. More than 200 bird species, including 80 kinds of water birds and four endangered species, regularly feed, rest, or nest on the refuge or other areas around the bay.

The bay provides habitat for approximately 100 species of fish, many of which contribute to sport or commercial fisheries, and provides habitat for steelhead, Coho, and Chinook salmon. The refuge also administers the Lanphere Dunes Unit and Castle Rock National Wildlife Refuge. Lanphere Dunes contains the most pristine remaining dune ecosystem in the Pacific Northwest and supports rare and representative examples of older forested dunes, young active dunes, dune swale wetlands, and coastal salt marsh.

Castle Rock Refuge is a 14-acre island located less than 1 mile off the Pacific Coast near Crescent City. The island serves as the second-largest seabird nesting colony south of Alaska. Castle Rock Refuge has the largest breeding population of common murres in California.

Each spring, over 20,000 Aleutian Canada geese roost on the island from late January through early April. Castle Rock Refuge also serves as a haul out for resting marine mammals including harbor seal, northern elephant seal, California sea lion, and Stellar's sea lion.

Humboldt Bay Refuge has a great diversity of wetland habitats in and adjacent to the Bay. In order of relative abundance they include mudflats, eelgrass beds, diked seasonal wetlands, sand spits, uplands, saltmarsh, brackish marsh, and freshwater marsh. Refuge habitats include seasonal wetlands, salt marsh, tidal mudflats and channels, open water, and uplands.