The 3,300-acre site is now part of the San Pablo Bay National Wildlife Refuge.
This morning's celebration included raising a white flag with an image of a blue goose, the symbol of the San Pablo Bay National Wildlife Refuge, U.S. Fish and Wildlife Service spokesman Doug Cordell said.
The U.S. Fish and Wildlife Service acquired the site on March 31, Cordell said this morning.
The San Pablo Bay National Wildlife Refuge lies along the north shore of the bay in Sonoma, Solano and Napa counties. It includes tidal marsh, mud flats and seasonal and managed wetland habitats.
It is the winter habitat for shore birds and waterfowl, including diving ducks, and is the year-round habitat for endangered and threatened species including the California clapper rail, salt marsh harvest mouse, California black rail, San Pablo song sparrow and Suisun shrew.
Nearly a dozen fish species swim through the San Pablo Bay to reach freshwater spawning grounds.
Skaggs Island was converted in the 1940s to a secret Navy facility. The Navy vacated the site, which contained more than 100 buildings, in 1994 and cleanup operations continued until 2000.
Among those scheduled to participate in this morning's 10 a.m. flag-raising ceremony were U.S. Fish and Wildlife Service Acting Director Rowan Gould, Deputy Assistant Secretary of the Navy Roger M. Natsuhara, and Congresswoman Lynn Woolsey.
Woolsey, who announced her retirement Monday, was involved in the negotiations to transfer the former Navy facility to the U.S. Fish and Wildlife Service and restore the site to tidal wetlands.
The demolition of a 12-story water tower on the site in January 2010 was symbolic of that restoration.