Humboldt Bay and its tidal sloughs are open to fishing year-round.
A protected area in the bay is the Humboldt Bay National Wildlife Refuge, created in 1971 for the protection and management of wetlands and bay habitats for migratory birds.
The Humboldt Botanical Garden, at the College of the Redwoods near the Bay, preserves and displays local native plants.
Humboldt Bay is also recognized for protection by the California Bays and Estuaries Policy.

In the winter, the bay serves as a feeding and resting site for more than 100,000 birds.
 Birds found on the bay include gull species, Caspian tern, brown pelican, cormorant, surf scoter, and common murre.

The bay is a source of subsistence for a variety of salt-water fish, crustaceans, and mollusks.
Sport fishing is permitted.
Dungeness crab are fished commercially, and oysters are commercially farmed in the bay.
The bay supports more than 100 species of marine and estuarine fish, including green sturgeon, coho and Chinook salmon, steelhead and coastal cutthroat trout, which spawn and rear in its watershed, covering an area of 223 square miles (580 km²).
 Coho salmon primarily rear and spawn in Elk River, Freshwater Creek, and Jacoby Creek.
A recent study found that 40% of coho in the system rear in the estuary.
The federally endangered tidewater goby is found in the bay, along with more common three-spined stickleback, shiner perch and Pacific staghorn sculpin.

The bay has been invaded by the European green crab, a voracious predator that is known to prey on the young of native crab species, as well as native mussels, oysters, and clams.
The invasive European green crab were first documented in Humboldt Bay in 1995 and have been blamed for a decline in clam harvesting.
Scientists have not found a way to control them.

Marine mammals are represented by harbor porpoises, harbor seal, California sea lion and river otter, with Steller sea lion and gray whale found immediately offshore.
Leopard sharks have been reported inside the bay, which also provides habitat for young bat rays, feeding on clams, crabs, shrimps, worms, sea cucumbers, brittle stars, various gastropods and isopods.
Humboldt Bay and its tidal sloughs are open to fishing year-round. A protected area in the bay is the Humboldt Bay National Wildlife Refuge, created in 1971 for the protection and management of wetlands and bay habitats for migratory birds. The Humboldt Botanical Garden, at the College of the Redwoods near the Bay, preserves and displays local native plants. Humboldt Bay is also recognized for protection by the California Bays and Estuaries Policy.
In the winter, the bay serves as a feeding and resting site for more than 100,000 birds.  Birds found on the bay include gull species, Caspian tern, brown pelican, cormorant, surf scoter, and common murre.
The bay is a source of subsistence for a variety of salt-water fish, crustaceans, and mollusks. Sport fishing is permitted. Dungeness crab are fished commercially, and oysters are commercially farmed in the bay. The bay supports more than 100 species of marine and estuarine fish, including green sturgeon, coho and Chinook salmon, steelhead and coastal cutthroat trout, which spawn and rear in its watershed, covering an area of 223 square miles (580 km²).  Coho salmon primarily rear and spawn in Elk River, Freshwater Creek, and Jacoby Creek. A recent study found that 40% of coho in the system rear in the estuary. The federally endangered tidewater goby is found in the bay, along with more common three-spined stickleback, shiner perch and Pacific staghorn sculpin.
The bay has been invaded by the European green crab, a voracious predator that is known to prey on the young of native crab species, as well as native mussels, oysters, and clams. The invasive European green crab were first documented in Humboldt Bay in 1995 and have been blamed for a decline in clam harvesting. Scientists have not found a way to control them.
Marine mammals are represented by harbor porpoises, harbor seal, California sea lion and river otter, with Steller sea lion and gray whale found immediately offshore. Leopard sharks have been reported inside the bay, which also provides habitat for young bat rays, feeding on clams, crabs, shrimps, worms, sea cucumbers, brittle stars, various gastropods and isopods.
Humboldt Bay