Colin Beddoes McNaughton was the son of H.H. McNaughton, assistant commissioner in the Ministerial Department of Crown Lands and Public Works (which included the Forestry Service) of the Cape Colony. He started his career in the civil service of the Cape Colony in 1888 or early in 1889 as a clerk in the crown land office. In September 1889 he became clerk and assistant to the conservator of forests of the Western Conservancy. He appears to have been stationed at Tokai, near Cape Town, but was appointed district forest officer at Campbell, Griqualand West, from July 1890 and transferred to the Midlands Conservancy in January 1891 and to the Western Conservancy in November that year. In August 1892 he became the first candidate to be selected for training in forestry at the Royal Indian Engineering College at Cooper's Hill, outside London, followed by practical training in the German and French Departments of Forestry. Upon his return he was appointed assistant conservator of forests in the Midland Conservancy in September 1894, and promoted to conservator there in 1898. In December 1902 he also became acting inspector of mines and diggings at Knysna. He remained in his post until he was pensioned under the retrenchment scheme of 1909, just before the formation of the Union of South Africa.
Soon after his return from overseas McNaughton wrote a Memorandum on the sand dunes of Gascony (Cape Town, 1895, 32p), indicating that he probably spent some time in Gascogne, France. In 1902 he published a substantial article on "Blue gums as forest trees" in the Agricultural Journal of the Cape of Good Hope (Vol. 21, pp. 567-588). It dealt with the success of Eucalyptus globulus at the Outiniqua plantations; the growth, characteristics, uses and value of the trees; and matters such as the required climate and soil. He was an early member of the South African Association for the Advancement of Science, from 1903 to at least 1906.
In 1903 McNaughton applied for four plots at Knysna. Between 1909 and 1917 he was involved in several legal cases relating to his debts. In December 1916, during World War I (914-1918), he was appointed as a temporary inspector of works in the Royal Engineers, with the honorary rank of lieutenant. He appears to have been employed in the Department of Agriculture of the Union of South Africa in 1919.