Mr Waugh continued at the university throughout four sessions prior to his entering on his theological studies, during which he attended the Latin, Greek, and Natural and Moral philosophy classes. He subsequently studied and acquired a competent knowledge of Hebrew. At the end of this period, he was examined by the presbytery regarding his proficiency in philosophy and the learned languages, and, having been found qualified was admitted to the study of divinity, which he commenced in August, 1774, under the tuition of the Rev John Brown of Haddington. Three years afterwards, he repaired to the university of Aberdeen, and attended for one session the lectures of Dr Beattie, professor of moral philosophy, and of Dr Campbell, professor of divinity in the Marischal college. In the following year, having been found amply qualified by prior attainments, he received his degree of M. A. On the completion of his studies, Mr Waugh was licensed to preach the gospel by the presbytery of Edinburgh at Dunse, June 28, 1779, and in two months afterwards was appointed by the presbytery to supply the Secession congregation of Wells-street, London, left vacant by the death of the Rev. Archibald Hall. On this occasion he remained in London for about ten weeks, when he returned to Scotland, and soon after received a unanimous call from the congregation of Newton, which was sustained by the presbytery at their meeting on December 21, 1779, and on the 30th of August, 1780, he was formally inducted to this charge.

The effects of the favourable impression, however, which he had made upon his hearers in London reached him, even in the retired and obscure situation in which he was now placed. A call to him from the Wells-street congregation was brought before the Synod which met at Edinburgh in May, 1781, but he was continued in Newton by a large majority. He himself had declined this call previously to its being brought before the Synod, and that for reasons which strikingly exhibit the benevolence of his disposition and the uprightness of his character. Amongst these were the unsettled state of his congregation, which was yet but in its infancy, the strong attachment which they had manifested to him, and the struggles which they had made for the settlement of a minister among them. But so desirous were the Wells-street congregation to secure his services, that, undeterred by the result of their first application, they forwarded another call to him, which was brought before the Synod on the 27th November, 1781, when it was again decided that he should continue at Newton. The second call, however, was followed by a third from the same congregation, and on this occasion the call was sustained by the presbytery on the 19th March, 1782. Mr Waugh received at the same time a call from the Bristo-street congregation of Edinburgh, but, owing to some informality, it did not come into direct competition with the former, and therefore was not discussed.

The presbytery of Edinburgh having been appointed to admit him to his new charge, this ceremony took place at Dalkeith on the 30th May, 1782; and in June following he set out for London, where he arrived on the 14th of that month, and immediately commenced his ministry in the Secession church, Wells-Street. He soon extended the reputation, which he had already acquired, amongst the body of Christians in London to which he belonged, and became exceedingly popular, at once by his singularly amiable character, his unwearied activity and unremitting zeal in the discharge of his ministerial duties, and by his fervid and impressive eloquence in the pulpit. He also took an active part in promoting the interests of the London Missionary and Bible societies; and even extended his benevolent exertions to many other religious and charitable institutions in the metropolis.

In 1815, he received the degree of doctor of Divinity from the Marischal college of Aberdeen, and was much gratified by this mark of distinction from that learned body, which he did not deem the less flattering, that, although he had studied there in his youth, he was, when it was conferred, almost an entire stranger, personally, to all of them. Previously to this, Dr Waugh had been seized with a serious illness, which had compelled him to revisit his native country, with the view of benefiting by the change of air. From this illness, he finally recovered; but, in May, 1823, he received an injury by the fall of some scaffolding, at the laying the foundation stone of the Orphan asylum at Clapton, from the effects of which he never entirely recovered. He, however, continued to preach with unremitting zeal, till the beginning of 1827, when increasing infirmities, particularly an inability to make himself audible in the pulpit, rendered it necessary to procure an assistant to aid him in his labours, as well on his own account, as on account of the spiritual interests of his congregation. In this year, therefore, he was relieved from a large portion of the laborious duties which had before devolved upon him. But this excellent man was not destined long to enjoy the ease which his affectionate congregation had kindly secured for him. In the last week of November, he caught a severe cold, which finally terminated his useful and active life, on the 14th of December, 1827, in the seventy-fourth year of his age, and the forty-fifth of his ministry in London.

The remains of Dr Waugh were attended to the grave by an immense concourse of people, drawn together on that melancholy occasion, by the celebrity and popularity of his character; and his congregation, as a testimony of their affection for his memory, erected an elegant tablet of marble, with a suitable inscription, in their chapel in Wells-street. They also claimed it as a privilege to defray the funeral expenses. But they did much more than all this: they secured an annuity for his widow, and expressed their sympathy in her bereavement, by many other acts of generosity and kindness.

Dr Waugh, in all the relations of life, was, perhaps, one of the most amiable men that ever existed. His character was pure and spotless; his benevolence unbounded; his philanthropy unqualified. His manners were mild, gentle, and highly prepossessing, and his piety sincere and ardent, and wholly without any portion of that gloominess which has been erroneously believed to belong to heart-felt religious feeling. So far from this, he was lively, cheerful, and humorous, and delighted in innocent mirth and raillery. To those of his countrymen, who came to London, his house and table were ever open; and his advice, counsel, and assistance in furthering their views, always at their service. His kindness in this way, indeed, he carried to an almost blameable extent.