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In 1790 his de facto convict wife Elizabeth Burley (also spelt Burleigh) gave birth to the first of their children, and in 1792 Arndell sought permission to retire on a pension so that he could pursue the life of a farmer. Initially granted 60 acres (24 hectares) of land in the Parramatta area by Governor Phillip, by 1806 he owned 630 acres (255 hectares), including a farm in the Windsor area given him by Governor King.
Arndell made his home in the Hawkesbury district where he served as a magistrate and acting surgeon to the area. As early as 1798 he had assisted the Reverend Samuel Marsden in an enquiry into the state of small-scale farming, and he maintained a keen interest in the welfare of the settlers in the Hawkesbury area and championed their grievances.
Arndell was a successful farmer, with large landholdings, running sheep and growing wheat. He reputedly built the first windmill in the Hawkesbury district for grinding flour. As a public figure he was loyal to a succession of governors, and sided with Governor Bligh against the officers of the New South Wales Corps. Under the military rule that followed the overthrow of Bligh he lost his magistracy and subsequently his pension. Macquarie was impressed with Arndell and was able to have his pension reinstated but Arndell did not continue with an active role in public administration. Arndell also contributed to the founding of a church at Portland Head and supported the Presbyterian church at Ebenezer.
The Arndells had a large family, all of whom had successful lives in the colony. Sarah, the third daughter of Thomas and Elizabeth, married the Reverend Lancelot Threlkeld who established a mission to the Aborigines in the Lake Macquarie area and subsequently became minister of the South Head Congregational Church. A daughter Arndell had fathered in England, Esther, married William Hovell in London and came with him to the colony. Hovell undertook the first explorations into the Port Phillip area.
Thomas Arndell died on 2 May 1821 and is buried in St Matthew's, Windsor, as is Elizabeth whom, according to Reverend Samuel Marsden, Arndell married in 1807. The site of his homestead at Cattai Farm is now part of Cattai National Park.
BH Fletcher, 'Arndell, Thomas (1753–1821)', Australian Dictionary of Biography, vol 1, Melbourne University Press, Melbourne, 1966, pp 27–28
Marjorie Raven, Assistant Surgeon Thomas Arndell: the man he was, the author, Bexley NSW, 1988