Moore was born to Peter Moore Smith, a military judge and army colonel, and Anne, a psychiatrist and social worker who emigrated from Dunoon, Scotland; she has a younger sister, Valerie, and brother, Peter Moore Smith, Jr. (born 1965). Her exact birthplace is not confirmed, and is sometimes stated as Fayetteville, North Carolina or Boston, Massachusetts. Growing up as an "army brat", she lived in twenty-three places across the United States and Germany. Moore attended Frankfurt American High School in Frankfurt, Germany, graduating in 1979. She received her Bachelor's degree at the School of Fine Arts in Boston University.
Moore moved to New York City in 1983, working as a waitress before being cast in the dual roles of Frannie and Sabrina Hughes on the soap opera As the World Turns, for which she won a Daytime Emmy Award; she played the roles from 1985 to 1988.
Moore began starring in feature films in the early 1990s, mostly appearing in supporting roles in films like The Hand That Rocks the Cradle, Benny and Joon with Johnny Depp, and The Fugitive. Her part in 1993's Short Cuts gained her critical acclaim and recognition, and she was cast in several high-profile Hollywood films, including 1995's romantic comedy Nine Months, and 1997's summer blockbuster The Lost World: Jurassic Park. Her role in the well-reviewed independent film, Safe, also attracted critical attention.
During the late 1990s and early 2000s, Moore appeared in a series of films that received Oscar recognition, including her roles in Boogie Nights ("Best Supporting Actress" nomination), The End of the Affair ("Best Actress" nomination) and her two 2002 films, Far From Heaven ("Best Actress" nomination) and The Hours ("Best Supporting Actress" nomination). During this period, she also appeared in the commercial successes Hannibal (controversially replacing Jodie Foster as Clarice Starling) and The Forgotten, and in Paul Thomas Anderson's follow-up to Boogie Nights, Magnolia.
Her film, Freedomland, opened in February 2006 to mixed reviews.
Her latest film Trust the Man is directed by her husband, Bart Freundlich and also features her son Caleb.
Moore is rumored to be reprising her role as Ian Malcolm's girlfriend, Dr. Sarah Harding in the film Jurassic Park IV which is set for release in summer 2008
Moore has been married three times: to Sundar Chakravarthy from November 21, 1983 to October 12, 1985, to John Gould Rubin from May 3, 1986 to August 25, 1995 and, since August 2003, to director Bart Freundlich. The couple, who have been together since 1996, have two children: a son, Caleb Freundlich (born December 4, 1997), and a daughter, Liv Helen Freundlich (born April 11, 2002). She is a noted pro-choice activist and during the last U.S. election donated money to John Kerry's presidential campaign.