During this period he had a part in building the Fish River Bridge, then the largest bridge in the country. He constructed the Queen's Road from Grahamstown to Fort Beaufort. Appointed Engineering Inspector by the Cape Roads Board in 1845 he began construction at Michell's Pass near Ceres in 1848, subsequently followed on completion by Bain's Kloof Pass near Wellington in 1853. He was the first man to attempt to build a road across the Limiet Mountains into the interior for which feat he was presented with table silver and a candelabrum by grateful colonists. Returning to the Eastern Cape in 1854, he built numerous roads and passes including the Katberg Pass near Fort Beaufort. This occupation created an interest in geology, inspired in 1837 by a copy of Lyell's "Elements of Geology". He was friendly with William Guybon Atherstone, who was also a keen geologist and fossil collector and who happened to be present at the discovery of "Paranthodon africanus" Broom at the farm Dassieklip on the Bushmans River, being about half-way between Grahamstown and Port Elizabeth. Bain discovered many fossil remains, including the herbivorous mammal-like reptile dicynodon "Oudenodon bainii Owen", which was excavated from the Karoo Beds on the farm Mildenhall south of Fort Beaufort and described in the literature by Sir Richard Owen. Among the specimens sent to Owen was the so-called Blinkwater monster, "Pareiasaurus serridens" as well as a variety of mammal-like reptiles. He was awarded £200 by the British government in 1845 for his researches. Devoting his spare time to geological studies, Bain prepared in 1852 the first comprehensive geological map of South Africa, a work of great merit, which was published by the Geological Society of London in 1856. Sir Roderick Murchison and Sir Henry de la Beche, prominent geologists of the time, both recommended Bain's appointment as Cape Geological Surveyor in 1852, but since no funds were available, nothing came of it. Bain went to Namaqualand in 1854 and reported to the Government on the copper mines there. He was granted sick leave to visit England for a second time in 1864, where he was entertained by Sir Richard Owen of the British Museum and Sir Roderick Murchison of the Royal Geographical Society, and was made an honorary member of the Athenaeum Club.