William Carruthers was born on May 29, 1830, in Moffat, Dumfriesshire, Scotland.

He was a Scottish botanist, paleobotanist, geologist, and agriculturalist. Educated at Moffat Academy, he graduated from the University of Edinburgh. In 1854, he began to study for the Presbyterian Ministry at New College, Edinburgh, but then decided to specialize in natural sciences. He became a lecturer in botany at the New Veterinary College in Edinburgh and served as assistant secretary to the Royal Society of Edinburgh. He became assistant in the Botany department of the British Museum in 1859, becoming Keeper of Botany in 1871 and retiring in 1895. Carruthers published scientific work on oaks, diatoms, mosses, fossil ferns, fossil Cycads, Calamites, and Lepidodendron. He was elected Fellow of the Royal Society in 1871. He was President of the Geologists Association of London from 1875 to 1877. He was President of the Linnean Society from 1886 to 1890 and a member of the Botanical Society of Edinburgh. He was awarded a Ph.D. by the University of Uppsala, Sweden in 1907. Carruthers was skeptical about Darwin's theory of evolution. In his 1876 presidential address to the Geologists Association of London, he argued that "the facts of paleontological botany are opposed to evolution". He was actively involved in the Presbyterian Church throughout his life. He was on its Committee on Publications (1880-1920) and edited the Children’s Messenger (1876-1921). He was keenly interested in the history of Puritanism.

In 1855, he married Jane Couch Moffatt (1838–1925). He died on June 2, 1922, in Surrey, England.