Most of the 11,000 acres of the reserve encompasses extensive seagrass meadows, tidal flats and sloughs, salt marshes, and upland forests and meadows. Key species include seagrass (Zostera marina and Zostera japonica), Dungeness crab, salmon, brant, bald eagle and peregrine falcon. Major activities at the reserve include research and education about Puget Sound. Research activities include characterizing and mapping major plant and animal communities, monitoring water quality and control of non-native species. Educational activities include free programs for people of all ages, free public exhibits, aquarium and trails.

Padilla Bay is about 70 miles north of Seattle near Anacortes, Wash.