Born in 1745, he lived most of his childhood in London,[1] but his father's work caused the family to travel widely: he was baptized in Portugal at the British Factory Chaplaincy, in Lisbon, on 27 August 1749;[2] educated at the University of Geneva in Switzerland.

[4] In November 1793, Margarot and Joseph Gerrald were chosen to attend the Edinburgh Convention organized by the Friends of the People Society - ostensibly a meeting for reformers, but seen as a threat and an attempt to establish an illegal government by William Pitt the Younger's ministry at the time.

The trial overseen by Thomas Elder in his capacity as Chief Magistrate of Edinburgh[5] in January 1794 was notable due to mob demonstrations in Margarot's favor.

Late in the voyage, Captain Patrick Campbell of the Surprize claimed to have been informed of a plan for mutiny and locked up several of the prisoners he was carrying, including Thomas Fyshe Palmer and William Skirving.

The source for this claim was information provided by this ships' superintendent of convicts William Baker, a British loyalist who had taken a strong dislike to the four Scotsmen.

Margarot fell into further trouble with authorities, for example, claiming at several points to have been appointed by the British government to report on the mis-governance of the young penal colony.

Months later, Governor Philip Gidley King seized Margarot's papers, which contained republican sentiments, evidence of conspiracy with the Irish, and a forewarning of Australia succeeding America as a chief power in the world.

[4][7] Following his and his wife's return to England, Margarot served as a witness in Parliamentary hearings concerning mis-governance and corruption in New South Wales (such as that which led to the Rum Rebellion), and his own sentence that he claimed was unjust in length.

[3] In the early years of the Chartist movement, Francis Place and others (including, earlier, Thomas Hardy) sought to rehabilitate Margarot's reputation, as plans went forwards for monuments to the martyrs in Edinburgh, and in London.