Willapa National Wildlife Refuge is located on the shores of Willapa Bay near the Pacific Ocean. The bay is one of the most pristine estuaries in the United States. From the protected bay, Chum, Chinook, and Coho salmon move to refuge streams to spawn.

The bay's shallow water and mud flats support vast beds of eelgrass and shellfish, providing spawning habitat for fish. During spring migration, more than 100,000 shorebirds are present. Isolated sandbars provide pupping grounds for harbor seals and rest sites for migratory birds.

Seabirds, such as brown pelicans, stream into the bay from the ocean in summer and fall. Other coastal habitats include sand dunes, sand beaches, and mud flats to grasslands, saltwater and freshwater marshes, and coniferous forest, including an old-growth stand of western red cedar-western hemlock forest.

Important species include the threatened marbled murrelet, bald eagles, great blue herons, and Brant. Grasslands and neighboring forests are home to bear, elk, bobcat, woodpeckers, flying squirrels, spotted owls, silver-haired bats, and Pacific tree frogs.

The Long Beach Peninsula protects the bay and its wildlife from storm winds and waves. Heavy rains swell the streams that carry nutrient-rich water and sediment to the bay. Chum, chinook, and coho salmon spawn in refuge streams. The bay's shallow water and mudflats support vast beds of eelgrass and shellfish. Eelgrass provides spawning habitat for fish and is the staple food of brant. During spring migration, more than 100,000 shorebirds are present. Isolated sandbars provide pupping grounds for harbor seals and rest sites for migratory birds. Seabirds, such as sooty shearwaters and brown pelicans, stream into the bay from the ocean in summer and fall.

Leadbetter Point, at the northern tip of Long Beach Peninsula, is a constantly-changing world of sand covered with patches of dune grass, lupine, wild strawberry, sand verbena, sea rocket, and beach pea. The bay side of the point contains some of the most significant saltmarsh habitats remaining in Washington.

Long Island's 5,400 acres of dense western hemlock, Sitka spruce, and western red cedar forest contain a 274-acre remnant of old growth lowland coastal forest. Some western red cedars in this grove have been growing over 900 years. The largest trees support nests of the threatened marbled murrelet. Bald eagles and great blue herons also nest here. Vast beds of eelgrass on the west side of the island provide important nurseries for Pacific herring, salmon, sea perch, and sole. Brant concentrate here in the spring.

The diked tidelands in the Riekkola Unit at the south end of the bay shelter and feed Canada geese, ducks, and shorebirds. These grasslands and neighboring forests are home to bear, elk, and bobcat. Standing dead trees contain nesting cavities for pileated woodpeckers, flying squirrels, and spotted owls. Roosting silver-haired bats and Pacific tree frogs find cover in the loose bark of old trees. The Lewis and Porter's Point Units provide freshwater marsh habitat for waterbirds, amphibians, anadromous fish, and aquatic mammals.