Michaelmas term 1832 he took a first class in classics and a second in mathematics, his friends were disappointed because he missed a double first. At Easter 1833 he was elected fellow of Oriel, took holy orders, and was at once appointed mathematical lecturer, and afterwards tutor of the college. At Oriel he fell under the influence of Newman, and became his devoted disciple. In February 1839, after wintering in the south of Europe, he assumed the office, at the invitation of Bishop Otter, of principal of the Diocesan Theological College at Chichester. After two years' conscientious work his health obliged him to resign, and returning to Oriel he was appointed sub-dean of the college in October 1841. By Newman's advice he declined in the same year Bishop Selwyn's invitation to accompany him to New Zealand.
Marriott watched with the utmost concern Newman's gradual alienation from the church of England, and when the catastrophe came in 1845 he, to a great extent, took Newman's place in Oxford. Newman had described him in 1841 as ‘a grave, sober, and deeply religious person, a great reader of ecclesiastical antiquity; and having more influence with younger men than any one perhaps of his standing.’ Marriott joined himself heartily to Dr. Pusey, and his high reputation rendered him an invaluable ally. There was, moreover, no doubt about Marriott's unshaken loyalty to the university. ‘For my own part,’ he said in 1845, ‘though I may be suspected, hampered, worried, and perhaps actually persecuted, I will fight every inch of ground before I will be compelled to forsake the service of that mother to whom I owe my new birth in Christ, and the milk of His word. I will not forsake her at any man's bidding till she herself rejects me.’ He became the correspondent and spiritual adviser of many, especially young men, and probably did as much as any one to stem the current that was setting towards Rome. In 1850 he was appointed vicar of St. Mary the Virgin, which was in the gift of his college, and was the university church. He threw himself with his wonted thoroughness into his parochial work. When the cholera and the small-pox both broke out at Oxford in 1854, he fearlessly visited the sufferers and caught the latter disease himself. Though he was no orator, his sermons were always effective.
Meanwhile he made great efforts to establish a hall for poor students. He acquired possession of Newman's buildings at Littlemore in order to prevent them from being turned into a Roman catholic establishment, and used them for a printing-press for religious works, a scheme which caused him endless worry and expenditure. He also threw himself into a commercial scheme at Oxford, termed ‘The Universal Purveyor,’ a sort of anticipation of the co-operative principle of the present day. It was started for the most benevolent purposes, but was quite out of Marriott's experience, and was a fruitful source of anxiety. He was at the same time a member of the hebdomadal council, and ‘took a considerable part in working the new constitution of the university’ (Church). The variety and pressure of his work shattered his health. On 30 June 1855 he had a stroke of paralysis. On 23 Aug. he was removed to Bradfield, Berkshire, where his devoted brother John was curate, and there he lingered for three years. He died 15 Sept. 1858, and was buried in a vault belonging to the rector under the south transept of Bradfield parish church.
Marriott's reputation was out of all proportion to his acknowledged literary work, but he did a vast amount of really valuable literary work, in connection with which his name did not appear. In 1849 he published ‘Reflections in a Lent reading of the Epistle to the Romans;’ in 1843 ‘Sermons preached before the University and in other Places;’ and in 1850, ‘Sermons preached in Bradfield Church, Oriel College Chapel, and other Places.’
Besides numerous single sermons, letters, and pamphlets (1841 to 1855), he also published ‘Two Lectures delivered at the Theological College, Chichester,’ 1841, and ‘Hints to Devotion,’ 1848. After his death his brother John edited his ‘Lectures on the Epistle to the Romans,’ 1859. They were delivered at St. Mary's during the last two years of his incumbency, and were the only results of what he intended to be the great work of his life, ‘a commentary on the Epistle to the Romans,’ which was to be his contribution to a commentary on the Bible projected by Dr. Pusey but never completed. From 1841 to the time of his seizure he edited, in conjunction with Pusey and Keble, ‘The Library of the Fathers.’ The lion's share of this vast undertaking fell upon Marriott. Dr. Pusey, in the advertisement to vol. xxxix., while paying a graceful tribute to his departed friend, frankly owned that ‘upon Charles Marriott's editorial labours “The Library of the Fathers” had, for some years, wholly depended.’ In 1852 he also edited, as part of a series of the original texts of the fathers, Theodoret's ‘Interpretatio in omnes B. Pauli Epistolas,’ and in May 1855 he became the first editor of ‘The Literary Churchman,’ in the first seven numbers of which he wrote at least sixteen articles.