The earliest evidence of human occupation of this area comes from artifacts recovered from "kitchen middens" located in the park. Native Americans who settled this area, gathered food from the ocean and lake. Fragments of bones, shell and pottery were discarded in refuse piles or "middens."

In the early 1900s, Munyon Island was famous for its lavish resort hotel, "The Hygeia." Built by Dr. James Munyon, the hotel was destroyed by fire in 1915. Munyon Island is not open to the public, but only accessible by boat.

The park is named after the previous property owner, John D. MacArthur, who wished to preserve it for future generations to enjoy. In the 1970s, after a university study convinced MacArthur that the property was a biological treasure, he donated a section for use as a public park. The John D. and Catherine T. MacArthur Foundation contributed additional funds to help develop the park and Nature Center. Facilities opened to the public in 1989.