John married Catherine Morgan on 14 November 1774 at Shipton under Wychwood, Oxfordshire. They had 3 children: Mary (b. 1775- d. ????),Hannah (b. 1778- d.???? ) and her twin, Anne (b. 1778- d.???? ); they were all baptised at Whichford.
1793 saw the construction of a mill at Sydney. David Collins stated:
John Baughan, an ingenious man, formerly a convict, had undertaken to build another mill upon a construction somewhat different from that of Wilkinson's, in which he was assisted by some artificers of the regiment. Both these mills were to be erected on the open spot of ground formerly used as a parade by the marine battalion.On 24 December 1793, the millwright and Baughan had got up the frame and roof of his mill-houses and, while waiting for there being tiled, was proceeding with preparing the wood-work of his mill. February 1794 saw the laying of tiles on the mill-house. The grinding mill commenced operations on the 10 March 1794; with nine men working its capstan bar, it ran so smoothly that sixty-three pounds (29 kg) of wheat were ground in seventeen minutes. James Wilkinson's mill near by, powered by six men who walked inside a massive wheel, commenced operations a month later; it was soon abandoned and Baughan was commissioned to replace it by another of his own design.
In recognition of his achievements as carpenter and millwright, Baughan was granted a small lease near Dawes Point. Here he erected and furnished 'a neat cottage', later acquired by Robert Campbell, and established an attractive garden. On 4 February 1796, overhearing himself being abused by a sentinel who apparently bore him an ancient grudge, Baughan slipped out of his workshop, collected his traducer's arms from his deserted post and handed them to the guard. The sentinel was immediately arrested. Next morning, as an act of reprisal, Baughan's cottage was stormed and extensively damaged by a military rabble. He and his wife 'suffered much personal outrage'. They were so sudden in the execution of this business, that the mischief was done before any steps could be taken either by the civil or military power to prevent it.
Baughan, after some days had elapsed, swearing positively to the persons of four of the principals in this transaction, a warrant was made out to apprehend them; but before it could be executed, the soldiers expressing themselves convinced of the great impropriety of their conduct, and offering to indemnify the sufferer for the damage they had done him, who also personally petitioned the Governor John Hunter in their behalf, the warrant was withdrawn.
It was observed, that the most active of the soldiers in this affair had formerly been convicts, who, not having changed their principles with their condition, thus became the means of disgracing their fellow-soldiers.