The Long Beach Peninsula separates Willapa Bay from the greater expanse of the Pacific Ocean.

With over 120 square miles (310 km2) of surface area Willapa Bay is the second-largest riverine estuary on the Pacific coast of the continental United States.

It is a ria, which formed after the rise in sea level at the end of the last ice age flooded several small river valleys.

The bay's ecology was threatened in the 1990s 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.

The State of Washington has been spraying an herbicide thought not to threaten other species since about 2005, and the Spartina threat is much reduced.