Early in 1808 Rev. Samuel Marsden, in search of two additional chaplains, came to Cowper's parish and invited him to accept appointment. He was willing and received a commission as an assistant chaplain in New South Wales at a salary of £260. His departure from England was delayed by the death of his wife, then the mother of three sons, including Charles, later a leading politician, and one daughter. Cowper married Ann Barrell, and sailed with his family to Port Jackson, arriving in August 1809. He took up duties as minister of St Philip's Church, then being completed. For the first ten years of his ministry, he was the only clergyman permanently in Sydney. Cowper arrived at Sydney on 18 August 1809 and became an assistant chaplain. He was also incumbent of
St Phillip's Church (the name was spelt this way in honour of the first
Governor of New South Wales,
Arthur Phillip). He found the state of morality in Sydney deplorable and actively set to work by preaching and, by example, to bring about an improvement. He was one of the founders and secretary of the
Benevolent Society of New South Wales and was at one time the secretary of six religious and charitable societies. In 1842 Cowper's eyesight began to fail; he obtained leave of absence to go to London to have an operation and was presented with a purse of £780 by his parishioners to cover his expenses. He returned in 1843 with his sight much improved and with a
Lambeth degree of Doctor of Divinity which had been conferred on him by the
Archbishop of Canterbury. In 1848 Cowper was instrumental in starting the building of the new church of St Philip and gave £500 towards the cost of it. In 1849 he had a dangerous illness but recovered, and in 1852 was appointed to administer the diocese during the absence of
Bishop Broughton on a visit to England. The bishop died in February 1853 and Cowper had to continue his duties until
Bishop Barker arrived in May 1855. ==Late life==