Early in her career, Hawes featured in at least four music videos, for the singles "Saturday Night" by Suede, "Marvellous" by The Lightning Seeds, "Come Around" by The Mutton Birds, and "She's a Star" by James. She first came into the public eye in the 1990s, having supporting roles in Troublemakers, Dennis Potter's Karaoke (1995), Heartbeat (1995), The Beggar Bride (1997), and as the young Diana Dors in the biopic The Blonde Bombshell (1999).

Hawes appeared in several BBC adaptations of classic and modern literature, including Our Mutual Friend (1998), Wives and Daughters (1999), Tipping the Velvet (2002).

Hawes married the DJ and Cartoonist Spencer McCallum in December 2001, when their son was almost two years old. They divorced in 2004. In November 2004, Hawes married Matthew Macfadyen, her Spooks co-star. Their first child, a daughter, was born in December of that year. Their second child, a son, was born in September 2006.

In 2002, after working on the television adaptation of Tipping the Velvet, Hawes was quoted in interviews with Diva magazine and Radio Times as saying that she is bisexual. Later, in a Daily Mail article, she explained that "what I actually said was that everybody is probably perfectly capable of finding somebody of the same sex attractive, but I certainly haven't had any lesbian relationships", and in Radio Times, she said "maybe what I meant is that everyone is a little bit bisexual … I've been married twice, both times to men".

In 2007, Hawes was cast as Alex Drake in Ashes to Ashes, the spin-off from the hit BBC series Life on Mars. It told the story of a female police officer in Service with London's Metropolitan Police, who, after being shot in 2008, inexplicably regains consciousness in 1981, having assimilated Sam Tyler's fantasies after being imprisoned in a coma. The series, broadcast in 2008, follows her fighting to wake up from the world of 1981 so she can get back to the present day and save her daughter. She was awarded the Best UK Television Actress Award in 2008 by the Glamour Awards for her role. In September 2009, Hawes filmed the final series. The finale aired in May and gained over seven million viewers.

Hawes won the "Glamour Best UK Television Actress Award" in 2008 for her role in Ashes to Ashes. She was also nominated for a TV Choice Award for the same role, and for the Best Actress award at the 2009 Crime Thriller Awards. She received a Leading Actress nomination for her role on Line of Duty for the 2015 British Academy Television Awards but ultimately lost out to Georgina Campbell.

On 25 April 2011, Hawes narrated the documentary Kate and William: A Royal Love Story on BBC One, prior to the wedding of Prince william and Kate Middleton. On 20 June 2011, she narrated the ITV1 documentary Four of a Kind as part of ITV's Extraordinary Families season. She appeared as Catherine Mundi in the fantasy adventure film Mariah Mundi and the Midas Box.

Hawes began working with UNICEF in 2012; in 2017 she became a UNICEF ambassador. Her main focus has been visiting children and families living in the Za’atari refugee camp and host communities in Amman. Many of these children and families had fled their homes in Syria due to the ongoing conflict.

In 2014, she starred as Detective Inspector Lindsay Denton in the second series of the BBC Two drama Line of Duty, giving what The Daily Telegraph described as "the performance of 2014". In the autumn of 2014, she guest-starred as Ms. Delphox in the eighth series of Doctor Who.

In July 2017, Hawes appeared in a television advert promoting the 'All new Ford Fiesta'.