Bonney was born in Rugeley, Staffordshire, England, the eldest son of the Reverend Thomas Bonney, headmaster of Rugeley Grammar School.[2] His uncle was the Australian explorer Charles Bonney, and one of his brothers, Frederic Bonney, is remembered for his photography and ethnology in Australia.[3] Thomas was educated at Uppingham School and St John's College, Cambridge, where he graduated as 12th wrangler in 1856, and was ordained in the following year.[2]
From 1877 to 1901 he was professor of geology in University College London. He became secretary and later president of the Geological Society of London (1884–1886), and also a fellow; secretary of the British Association (1881–1885) and its president[4] for the year 1910–1911; president of the Mineralogical Society. He was president of the Alpine Club, 1881–1883. In 1887, Bonney was appointed honorary canon of Manchester.
He was elected a Fellow of the Royal Society on 6 June 1878.[5] He died in Cambridge on 10 December 1923. Lake Bonney in Antarctica is named after him.