On the 10th July, 1792, Surgeon Arndell requested Governor Phillip to permit him to retire from the service 'with such small part of my pay as my services in this country may be thought to merit, and that the land, which I have begun to cultivate, with a view to becoming a settler, may be granted me for the purpose.'
In a despatch written to Lord Dundas on 4th August, 1792, Phillip reported that he had granted 60 acres of land to Arndell who had about ten acres of land in cultivation at his own expense. 'He continues to do his duty at Parramatta, where he has had the direction of the hospital for near three years, and will be continued in that charge until he receives permission to retire.' Lord Dundas informed Lieut.-Governor Grose in correspondence dated 31st June, 1793 that the surgeon had been granted permission to retire on a pension of £50 per annum.
Thomas Arndell took up his residence at his farm on Northern Boundary, which was known as Arthur's Hill. In 1799 he obtained a second grant of 100 acres north of Carlingford adjoining the grant made to Francis Oakes and known as Home Farm.
He became a Magistrate and Justice of the Peace first at Parramatta in 1799 and later in the Hawkesbury district.
His connection with Parramatta ceased in 1817. In the Sydney Gazette in July, 1817, Simeon Lord advertised 'All that desirable and well known farm in two grants, known by the name of Arndell's farm in the district of Northern Boundary, 60 acres of which have been cleared. 
On 14th June, 1804 Thomas Arndell obtained a grant of 600 acres of land from Governor King. The land lies at the junction of the Cattai Creek and Hawkesbury River. Here he resided until his death, in 1821.
Arndell's pension was stopped after the departure of Governor King, in 1806, and it was not restored until 1812, when he received arrears of £300. In endorsing a memorandum of Arndell's on the subject, Governor Macquarie stated: 'This gentleman is now far advanced in years, and has a wife and a numerous family of children to provide for, whom he has brought up, and educated, in a most, respectable way; but his means of support arising altogether from the produce of his farm are very inadequate to this object. I beg to assure your Lordship that in point of character he is a very honest man, and, a very loyal subject, and I conceive in every point of view fully deserving the indulgence he now solicits.' 
Thomas Arndell (sen.,) died on 2nd May 1821. The Sydney Gazette announced his death.....Died on Wednesday night last, at his residence, at Cattai Creek, on the bank of the Hawkesbury River, Thomas Arndell, Esq., after a painful illness of five weeks. This gentleman came to these shores with the First Fleet in 1788, as a surgeon, and, for a number of years, held the high and responsible position of magistrate in the town of Windsor. He has exceeded his seventieth year, and has died much lamented 
Rev. Samuel Marsden conducted the funeral service in St. Matthew's Church, Windsor on Sunday, 6th May1821. Thomas Arndell was interred in the burial ground at the church.
 Historical Records of Australia, Vol. I., p. 392., Vol. I., p. 392.
 Sydney Gazette 12 July 1817
 Historical Records of Australia, Vol. 7, p. 612
 Sydney Gazette 5 May 1821
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