After graduating Mehta began working for a production company that made documentary and educational films for the Indian government. During the production of her first feature-length documentary focusing on the working life of a child bride, she met and married Canadian documentary filmmaker Paul Saltzman, who was in India making a film. She migrated to Toronto to live with her husband in 1973.

In Canada she met and married filmmaker Paul Saltzman whom she divorced in 1983. The couple have a daughter, Devyani Saltzman, an acclaimed author, curator and cultural critic.

Mehta also directed the documentaries At 99: A Portrait of Louise Tandy Murch (1975) and Traveling Light (1986), the latter focusing on the work of Mehta’s brother Dilip as a photojournalist. Traveling Light would go on to be nominated for three Gemini Awards. In 1987, based on the works of Alice Munro, Cynthia Flood and Betty Lambert, Mehta produced and co-directed Martha, Ruth and Edie. Screened at the Cannes International Film Festival, it would go on to win the Best Feature Film Award at the 11th International Film Festival in Florence in 1988.

In 1991 she made her feature-film directorial debut with Sam & Me (starring Om Puri), a story of the relationship between a young Indian boy and an elderly Jewish gentleman in the Toronto neighbourhood of Parkdale. It broke the record at the time for the highest-budgeted film directed by a woman in Canada at $11 million. It won Honorable Mention in the Camera d’Or category of the 1991 Cannes Film Festival. Mehta followed this with her film Camilla starring Bridget Fonda and Jessica Tandy in 1994. In 2002, she directed Bollywood/Hollywood, for which she won the Genie Award for Best Original Screenplay.

Mehta directed two episodes of George Lucas’ television series The Young Indiana Jones Chronicles. The first episode, “Benares, January 1910”, aired in 1993. The second episode was aired in 1996 as part of a TV movie titled Young Indiana Jones: Travels with Father.

Water is the story of an eight-year-old child widow who is forced to enter a house of widows for the rest of her life. The film, meant to be shot in India, was attacked by Hindu fundamentalists who saw the film as disrespectful and who took issues with Mehta’s earlier films and their portrayal of Hindu culture. Riots broke out, sets were destroyed, and death threats were issued towards the actors and Mehta, forcing production to stop. The regional government then overruled the permission given from the central government to the production which allowed them to film in the holy city of Varanasi however, four years later the movie was made in Sri Lanka. Water opened the 2005 Toronto International Film Festival and was nominated for an Academy Award for Best Foreign Language Film in 2006.

Mehta directed several English-language films set in Canada, including The Republic of Love (2003) and Heaven on Earth (2008) which deals with domestic violence and has Preity Zinta playing the female lead. It premiered at the 2008 Toronto International Film Festival. Also in 2008 Mehta produced the documentary The Forgotten Woman, directed by her brother Dilip.

The film was released on 9 September 2012 at Toronto International Film Festival and would be nominated for Best Motion Picture along with 7 other nominations at the Canadian Screen Awards.

In 2015, Mehta wrote and directed the crime thriller Beeba Boys (2015), a film starring Randeep Hooda as Jeet Johar, a proud observant Sikh and a ruthless gangster. It premiered at the 2015 Toronto International Film Festival.

On 29 October 2020, Telefilm Canada announced that Metha’s film Funny Boy (2020) would represent Canada in the Academy Awards race for best international feature film.