The refuge preserves several unique ecosystems, including diverse salt marshes, muddy tideflats, rain-drenched old growth forests, and dynamic coastal dunes and beaches. Freshwater marshes and grasslands are found along the southern shore of the bay.

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.

From Portland, three different routes will lead to the refuge: Highway 26 West to Highway 101 North; Interstate 5 North to Highway 4 West to Highway 101 South; or Highway 30 West to Highway 101 North.

Refuge Headquarters: From Seaview, take Highway 101 north. Ignore the large brown sign saying "Willapa National Wildlife Refuge" with an arrow pointing north up Sandridge Road (this would take you to the Riekkola and Leadbetter Units). Refuge headquarters is approximately 10 miles from Seaview, near mile post 24. A boat ramp on the left side of the highway offers the best departure point for Long Island.

Reikkola Unit: From Highway 101, turn north onto Sandridge Road just east of Seaview, Washington. At 67th Place, turn right (east). 67th Place becomes Yeaton Road, which dead-ends on the refuge.

Porter Point Unit:: From Highway 101, turn north onto Sandridge Road just east of Seaview, Washington. At 67th Place, turn right (east), 67th Place becomes Yeaton Road, which dead-ends on the refuge. Walk in from the refuge gate following the refuge road towards the north and Willapa Bay. Turn right to walk approximately 1.75 miles of dike road.

Leadbetter Unit: From Highway 101, turn north on Sandridge Road. Near Oysterville, jog west and continue north on Stackpole Road until the road ends at a parking lot on the edge of the refuge. It is approximately 20 miles from Highway 101 to the Leadbetter parking area. Note: The parking lot is owned by Washington State Parks and located on adjacent Leadbetter Point State Park. Washington State Parks charges a $5 parking fee unless you have a Washington Vehicle Use Permit. For information on obtaining parking pass, visit the Washington State Department of Fish and Wildlife Vehicle Use Permit Web site.

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These wetlands are managed to increase overwintering carrying capacity for Pacific brant in Willapa Bay; to maintain current capacity in support of overwintering waterfowl, with special emphasis on Canada geese, wigeons, and canvasbacks; and to provide for maximum use and production by other migratory birds, with special emphasis on bald eagles and marsh and wading birds. Spartina alterniflora (smooth cordgrass) invasion of refuge saltmarshes and mud flats is the biggest wetland issue confronting this refuge.

Introduced from the east coast, Spartina is rapidly invading the tidelands of Willapa Bay and destroying migratory bird, anadromous fish, and shellfish habitat as well as marine organism and saltmarsh communities. Cooperative work with State and other Federal agencies to control Spartina with mechanical methods and chemicals involves up to 50 people concentrating on this effort.

Water levels on the Lewis and Porter's Point Units are managed to provide abundant food for migratory waterfowl, rearing habitat for salmonids, and breeding habitat for aquatic amphibians. A cooperative farming agreement on about 300 acres of the Riekkola Unit, which involves grazing, haying, and pest plant control, is used to maintain foraging habitat for geese.

Grazing cattle in the summer create fields of short grass in fall for six subspecies of Canada geese, including the rare Aleutian and dusky. In recent years, marginal, poorly drained pastures have been removed from this management regimen. Where possible, these wetter sites are converted to freshwater marsh.

The refuge administers a Presidential Proclamation Boundary that closes a portion of Willapa Bay to waterfowl hunting.

Due to the degraded nature of refuge forests as well as those of the surrounding areas, a major effort is needed to restore these forests to a semblance of their natural state. The refuge has embarked on a landscape-based forest management program in cooperation with the Nature Conservancy, which manages the 7000 acre Ellsworth Creek Preserve which is located adjacent to the refuge. Forest inventories on both properties have been completed and a forest management plan is being developed. Activities to restore forests will include manipulation of degraded forest stands through such techniques as variable density thinning, direct reestablishment of under-represented tree and other plant species, removal of non-native species and elimination of unnecessary and deteriorating forest roads.