South Slough National Estuarine Research Reserve is located in a sheltered arm that forms the southern end of the Coos estuary in southwestern Oregon. The Reserve and its watershed protect a relatively undisturbed area representative of coastal ecosystems in the Pacific Northwest. Its uplands are characterized by steep slopes supporting conifer forests with stream systems supplying fresh water to the estuary. The lowlands support freshwater wetlands and ponds, high and low salt marshes that have experienced varying degrees of disturbance and recovery, emergent islands including Valino Island, sand and mud flats, and beds of eelgrass (both native Zostera marina, and the introduced Zostera japonica) which cover a significant portion of the Coos estuary substrate. The reserve is important habitat for salmon, great blue herons, bald eagles, migrating ducks, elk, sea otters, oysters and crabs.

The reserve is located five miles south of Charleston, Ore., on the South Slough of the Coos Bay estuary.