She received nominations for the Academy Award for Best Supporting Actress for Pollock (2000) and Mystic River (2003), winning for her portrayal of artist Lee Krasner in the former.

She received Primetime Emmy Award nominations for her guest roles in the crime drama series Law & Order: Special Victims Unit (2005) and the Apple TV+ series The Morning Show, and supporting role in the television film The Courageous Heart of Irena Sendler (2009).

Harden's family frequently moved because of her father's job, living in Japan, Germany, Greece, California, and Maryland.

Her notable film roles include the Disney sci-fi comedy Flubber (1997), a popular hit in which she co-starred with Robin Williams; the supernatural drama Meet Joe Black (1998), playing the under-appreciated daughter of a tycoon (Anthony Hopkins, co-starring Brad Pitt); Labor of Love (1998), a Lifetime television film in which she starred with David Marshall Grant; and Space Cowboys (2000), an all-star adventure-drama about aging astronauts.

In 2000, Harden won the Academy Award for Best Supporting Actress for her portrayal of painter Lee Krasner in the biographical film Pollock.

In 2004, she received a second Academy Award nomination for Best Supporting Actress for her performance in the mystery crime drama Mystic River.

Harden guest-starred as FBI undercover agent Dana Lewis posing as a white supremacist in "Raw", an episode of the popular crime drama Law & Order: Special Victims Unit.

Harden appeared in several 2007 films, including Sean Penn's Into the Wild and Frank Darabont's The Mist (opposite Thomas Jane and Laurie Holden), based on the novella by Stephen King.

Also in 2007, she shared top billing with Kevin Bacon in Rails & Ties, the directorial debut of Alison Eastwood.

Harden appeared as a regular on the FX series Damages as a shrewd corporate attorney opposite Glenn Close and William Hurt in 2009.

She received a 2009 Emmy nomination for her role in The Courageous Heart of Irena Sendler, a TV film also starring Oscar-winner Anna Paquin.

Harden returned to Broadway in Yasmina Reza's God of Carnage, co-starring with James Gandolfini, Hope Davis and Jeff Daniels, in 2009.