On the lagoon's northeastern and eastern edges in the park, there are saltwater and brackish marshes that support thriving bird populations.

Two of the Nine Sisters chain of volcanic peaks, Black Hill and Cerro Cabrillo, are within the park.

Black Hill has a trail through the Monterey Pine (Pinus radiata) trees in Flemings Forest.

The first settlers of the local area were of the Millingstone Horizon culture, early Chumash Native American peoples.

One of the closest local settlements of Chumash to Morro Bay State Park is the Back Bay site, a large Chumash archaeological site on a stabilized sand dune in Los Osos dating to at least as early as 800 to 1200 AD.