Willapa Bay is fairly shallow: more than half of its surface area lies in the intertidal zone, and in fact half of the volume of water inside it enters and leaves with every tide. The bay is an estuary formed when the Long Beach Peninsula, a long sand spit from the Columbia River to the south, partially enclosed the estuaries of several smaller rivers. The North River, Willapa River, and Naselle River provide most of the freshwater input into the bay.
The bay is bordered by several smaller towns and unincorporated communities such as Raymond, South Bend, and Tokeland. The bay is entirely located within Pacific County, Washington and is home to a local oyster and seafood processing industry: approximately 9% of all oysters in the U.S. are grown there.
Willapa Bay is known for its amazing biodiversity and much of it, including the entirety of Long Island, has been set aside as part of the Willapa National Wildlife Refuge. The oyster beds help the ecosystem by providing habitats and filtering water, improving the quality of the water. The bay's ecology is threatened by the rapid spreading of atlantic cordgrass (Spartina Alterniflora), a non-native species of grass introduced possibly to help preserve wetlands and marsh areas, and possibly simply by accident, as packing material in crates of oysters from the East Coast.