Siletz Bay NWR was established in 1991 primarily to return salt marsh to its natural state. Formerly it had been diked and crossed with ditches to create pasture for dairy cow grazing. More than 9,300 ft (2.8 km) of dikes were removed and a quarter mile (500 m) of ditch were filled to initiate restoration. Salt-starched skeleton trees are visible along both sides of U.S. Route 101 (which runs through the refuge) from the time when the salt marsh was diked. Red-tailed Hawks and Bald Eagles are often visible roosting on these snags. Abundant Great Blue Heron and Great Egret live nearby.

The refuge is located on Siletz Bay, immediately south of Lincoln City where the Siletz River enters the bay. It is closed to all public use, except during special events.