Cotton entirely identified himself with every aspect of Church work in the diocese of Bangor; he was secretary of the Christian Knowledge Society, chairman of the Bangor auxiliary of the British and Foreign Bible Society, a founder of the Bangor Church Building Society in 1838 and of the Caernarvon and Anglesey Hospital in May 1814. From the first he was regarded as an apostle of education; in 1810 he opened a Sunday school in the cathedral, and National schools at Pentir and Vaynol, then both in the parish of Bangor, and later also in the town of Bangor and the parishes of Llanllechid and Gaerwen; his activities embraced every side of school work — he founded schools, taught in schools, inspected schools honorarily, and defended the schools fearlessly in the press; when the celebrated Government education commission of 1846, whose report in 1847 earned the epithet ‘Brad y Llyfrau Gleision,’ inspected North Wales schools, he trenchantly exposed their methods as those of cross-examining counsel in the law courts and not of school inspectors.

In 1848 he became a member of the newly-founded Bangor Diocesan Board of Education to co-ordinate the work of various bodies in the diocese. As vicar of Bangor and cathedral precentor, the fabric of the cathedral and its services, English and Welsh, were his chief care, and in 1824-7 he effected a restoration and rearrangement of the interior, dividing it into a western church for Welsh parochial services and an eastern church for English cathedral services, and giving each language its full place, thus inaugurating the system still in force, although the restoration under Sir Gilbert Scott reversed his architectural arrangements.