He graduated Bachelor of Arts (BA) in 1815, being senior optime in the mathematical tripos and the first chancellor's medallist, and in 1816 he was member's prizeman.
He had in the meantime published (1822), in conjunction with Barnard Hanbury, his Journal of a Visit to some parts of Ethiopia, describing a journey from Wadi Halfa to Meroë and back.
In 1829 he issued a volume on The Present Condition and Prospects of the Greek or Oriental Church, with some Letters written from the Convent of the Strophades, which, when revised, was reissued in a new edition in 185.
About 1826, Waddington was ordained in the Church of England, and in December 1827 he preached the sermon in the chapel of Trinity College on Commemoration day.
He was presented by Trinity College to the perpetual curacy of St Mary the Great, Cambridge, on 1 February 1833, and on 17 June 1834 was presented by Trinity to the vicarage of Masham and Kirkby-Malzeard in Yorkshire, being also appointed on 1 October in that year commissary and official of the prebend of Masham.