She was valedictorian of her class at the Northrop Collegiate School (now The Blake School) in Minneapolis, graduating in 1970. She received a bachelor's degree in physics "summa cum laude", Phi Beta Kappa, from Colorado College in 1973. As a National Science Foundation Graduate Fellow, she then studied geophysics at the Scripps Institution of Oceanography where she earned a PhD in earth sciences in 1978. Her dissertation was titled "Continental and Oceanic Isostasy". McNutt is a National Association of Underwater Instructors (NAUI)-certified scuba diver and she trained in underwater demolition and explosives handling with the Underwater Demolition Team (UDT) of the United States Navy and the United States Navy SEALs.