Margaret Stoddart was born at Diamond Harbour, Canterbury. She was educated at Edinburgh Girls College and on her return to New Zealand studied at the Christchurch School of Art. She soon gained a local reputation as a watercolourist. In 1885 she was elected to the Council of the Canterbury Society of Arts and in 1889 she became a member of the Christchurch Palette Club.
From 1897 - 1906 Stoddart travelled to England, Italy, Capri, Norway and France. She spent some time in Cornwall studying under the American teacher Charles Lasal. Stoddart was also associated with the popular and influential Newlyn School. Along with other New Zealand expatriates she had some minor successes in Europe. Stoddart's works were exhibited in London at the Royal Academy and the Royal Institute, at the Paris Salon and the Society of Aquarellists in Rome.
She stayed and worked for a few years living on "a pound a week" and during this time met Frances Hodgkins who was living in similar circumstances.
She worked in Europe for a few years and then decided to return to Christchurch. From 1885 till her death in 1934 she remained on the council of the Canterbury Society of Arts and for fifty years was a leader in the Christchurch art circles.
Margaret Stoddart had a consuming passion for painting plants, both for botanical purposes and as an art form. Her numerous renditions of still life subjects show her ability as a painter. In the 1890s Margaret Stoddart was famous for her flower paintings. The Melbourne Argus described her as
'standing without a rival, the first and foremost of flower painters in Australia'.
A collection of watercolour studies of native flowers, originally meant for publication, is in the Canterbury Museum. She is represented at the Auckland Art Gallery, Museum of New Zealand, Waikato Museum of Art and History and major New Zealand galleries, including the Suter and the McDougall.