He studied medicine at Edinburgh, and, on obtaining his M.D. degree, joined the Royal Navy in 1848. He early attracted the notice of Sir Roderick Murchison, through whom he was appointed surgeon and naturalist to the Niger expedition sent out in 1854 by Macgregor Laird with government support. The death of the senior officer (Consul Beecroft) occurring at Fernando Po, Baikie succeeded to the command.
Ascending the Benue about 250 miles beyond the point reached by former explorers, the little steamer "Pleiad" returned and reached the mouth of the Niger, after a voyage of 118 days, without the loss of a single man. The expedition had been instructed to endeavour to afford assistance to Heinrich Barth, who had in 1851 crossed the Benue in its upper course, but Baikie was unable to gain any trustworthy information concerning him. Returning to the UK, Baikie gave an account of his work in his Narrative of an Exploring Voyage up the Rivers Kwora and Binue (1856).
In March 1857, Baikie—with the rank of British consul—started on another expedition in the "Pleiad". After two years spent in exploring the Niger, the navigating vessel was wrecked in passing through some of the rapids of the river, and Baikie was unable longer to keep his party together. The survivors of the expedition were not rescued from Africa for a year. The botanist, Charles Barter, who trained at Kew Gardens and was foreman of Regent's Park of the Royal Botanic Society, London from 1851-1857, caught dysentry and died at Rabba, Nigeria in 1859. He is commemorated by the genus Barteria Hook. f. in the Passifloraceae.
William Baikie, in no way daunted, determined single-handed to carry out the purposes of the expedition. Landing from a small boat, with one or two native followers, at the confluence of the Niger and Benue, he chose Lokoja as the base of his future operations, it being the site of the model farm established by the expedition sent by the British government in 1841, and abandoned within a twelvemonth on the death of most of the white settlers (see Capt. W. Allen, R.N., and T. R. H. Thomson, M.D., A Narrative of the Expedition . . . to the River Niger in 1841, (1848)).
After purchasing the site, and concluding a treaty with the Fula emir of Nupe, he proceeded to clear the ground, build houses, form enclosures and pave the way for a future city. Numbers flocked to him from all neighboring districts, and in his settlement were representatives of almost all the tribes of West-Central Africa. To the motley commonwealth thus formed he acted not merely as ruler, but also as physician, teacher and priest. In less than five years he had opened up the navigation of the Niger, made roads, and established a market to which the native produce was brought for sale and barter. He had also collected vocabularies of nearly fifty African dialects, and translated portions of the Bible and prayer-book into Hausa. Once only during his residence had he to employ armed force against the surrounding tribes. While on his way home, on leave of absence, he died at Sierra Leone.
William Baikie had three sons; John, Eddison and William and 5 daughters Elizabeth, Hannah, Joyce, Christine and Nicole. Eddison the second youngest moved to the Orkney islands before his fathers death; where he had 6 children William Annete Josephine John Patrick and Isaac. Isaac then had 5 children William Patrick Elizabetha and Isaac. Patrick then had 2 sons one of which was John robertson baikie, he married Emily joyce warne and had a daughter christine,,, she married William Thompson and they had 4 children; Stephen Katherine Mark and John. Stephen married Louise Destro and they had 3 children; Gemma Corinne and Ben. He had done much to establish British influence on the Niger, but after his death the British government abolished the consulate (1866), and it was through private enterprise that some twenty years later the district where Baikie had worked so successfully was finally secured for the UK (see Nigeria).
Baikie's Observations on the Hausa and Fuifuide (i.e. Fula) Languages was privately printed in 1861, and his translation of the Psalms into Hausa was published by the Bible Society in 1881. He was also the author of various works concerning Orkney and Shetland. A monument to his memory was placed in the nave of the ancient Cathedral of St Magnus, Kirkwall.