In 1827 he returned to Manchester College, York to teach Mathematics and philosophy. While he was there he became involved with the Philosophical Radicals. He stayed there until 1834 and in 1839 took a break from teaching to resume his work with the church, serving in 1845 as the minister at what later became Rosslyn Hill Unitarian Chapel in Hampstead. In 1849 he became the first professor of natural history at Queen's College, Cork, the same year as the college started teaching and 4 years after it was founded. While there he had a major role in the development of the botanical gardens, in which he hoped to represent all the known orders of plants that he could grow in the Irish climate. He was also involved in developing the museum and herbaria. In 1853 he travelled to Canada, where he became the first professor of natural history at University College, Toronto. This was a somewhat controversial appointment as he was chosen over Thomas Henry Huxley who had the backing of a number of well respected botanists including Charles Darwin. It was suspected that his success over Huxley was due to the influence of his brother Francis Hincks, who was Premier of the Province of Canada at the time. He was said to be well like by his students there, although his ideas and teaching style was often seen as outdated. He was strongly opposed to Darwinism, preferring the Quinarian taxonomic system.
Other work
Hincks was elected as a fellow of the Linnean Society, a society for the study of taxonomy and natural history, in 1826. In 1828, while teaching at Manchester College, York, he became the first Honorary Curator of Botany in the museum of the Yorkshire Philosophical Society. The society was formed in 1822 as a charitable organisation aimed at promoting the natural sciences, archaeology and history. Following the construction of the museum and its associated gardens, Hincks planned to organise the plants using de Candolle's system though only a small amount had been planted to this scheme by the time of his departure from the post. Hincks had spent most of time working with the herbarium collections rather than the gardens. While teaching and serving as a clergyman, Hincks also carried out editing and publishing work. He was the first editor of the Unitarian magazine The Inquirer from 1842 to 1847 during his time in London. His work there was influenced by his interest in education and his desire for an end to slavery and the death penalty. In Canada he served as president of the Canadian Institute from 1869 to 1871 and became editor of their journal, the Canadian Journal. Through this he published a number of books including:
Personal life
In 1817 Hincks married Maria Ann Yandell and together they had 8 children, five boys and three girls. One of their sons Thomas Hincks followed in his fathers footsteps and also became a minister and naturalist. Yandell died in 1849 and Hincks remarried Sarah Maria sometime before leaving England, her maiden name is not known. William Hincks died in Toronto on 10 September 1871 at the age of 77.