 Johnston returned to New South Wales in May 1813 as a private individual and in November the following year he married Esther Abrahams, a Jewish convict whom Johnston had met on the transport Lady Penrhyn in 1787, at St John's Church in Parramatta.The couple had already had seven children together by that time and they lived on his land at Annandale Farm, Sydney.He died much respected on 5 January 1823, leaving a large family.