Hutton was born in Edinburgh on 3 June 1726, as one of five children of Sarah Balfour and William Hutton, a merchant who was Edinburgh City Treasurer. Hutton’s father died in 1729, when he was three.

He was educated at the High School of Edinburgh (as were most Edinburgh children) where he was particularly interested in mathematics and chemistry, then when he was 14 he attended the University of Edinburgh as a “student of humanity”, studying the classics. He was apprenticed to the lawyer George Chalmers WS when he was 17, but took more interest in chemical experiments than legal work. At the age of 18, he became a physician’s assistant, and attended lectures in medicine at the University of Edinburgh. After three years he went to the University of Paris to continue his studies, taking the degree of Doctor of Medicine at Leiden University in 1749 with a thesis on blood circulation.

This developed his interest in meteorology and geology. In a 1753 letter he wrote that he had “become very fond of studying the surface of the earth, and was looking with anxious curiosity into every pit or ditch or bed of a river that fell in his way”. Clearing and draining his farm provided ample opportunities. The mathematician John Playfair described Hutton as having noticed that “a vast proportion of the present rocks are composed of materials afforded by the destruction of bodies, animal, vegetable and mineral, of more ancient formation”. His theoretical ideas began to come together in 1760. While his farming activities continued, in 1764 he went on a geological tour of the north of Scotland with George Maxwell-Clerk, ancestor of the famous James Clerk Maxwell.

Between 1767 and 1774 Hutton had close involvement with the construction of the Forth and Clyde canal, making full use of his geological knowledge, both as a shareholder and as a member of the committee of management, and attended meetings including extended site inspections of all the works. At this time he is listed as living on Bernard Street in Leith. In 1777 he published a pamphlet on Considerations on the Nature, Quality and Distinctions of Coal and Culm which successfully helped to obtain relief from excise duty on carrying small coal.

In 1768 Hutton returned to Edinburgh, letting his farms to tenants but continuing to take an interest in farm improvements and research which included experiments carried out at Slighhouses. He developed a red dye made from the roots of the madder plant.

He had a house built in 1770 at St John’s Hill, Edinburgh, overlooking Salisbury Crags. This later became the Balfour family home and, in 1840, the birthplace of the psychiatrist James Crichton-Browne. Hutton was one of the most influential participants in the Scottish Enlightenment, and fell in with numerous first-class minds in the sciences including mathematician John Playfair, philosopher David Hume and economist Adam Smith. Hutton held no position in the University of Edinburgh and communicated his scientific findings through the Royal Society of Edinburgh. He was particularly friendly with physician and chemist Joseph Black, and together with Adam Smith they founded the Oyster Club for weekly meetings.

In 1783 he was a joint founder of the Royal Society of Edinburgh.

Hutton developed several hypotheses to explain the rock formations he saw around him, but according to Playfair he “was in no haste to publish his theory; for he was one of those who are much more delighted with the contemplation of truth, than with the praise of having discovered it”. After some 25 years of work, his Theory of the Earth; or an Investigation of the Laws observable in the Composition, Dissolution, and Restoration of Land upon the Globe was read to meetings of the Royal Society of Edinburgh in two parts, the first by his friend Joseph Black on 7 March 1785, and the second by himself on 4 April 1785. Hutton subsequently read an abstract of his dissertation Concerning the System of the Earth, its Duration and Stability to Society meeting on 4 July 1785, which he had printed and circulated privately. In it, he outlined his theory as follows;

Though Hutton circulated privately a printed version of the abstract of his Theory (Concerning the System of the Earth, its Duration, and Stability) which he read at a meeting of the Royal Society of Edinburgh on 4 July 1785; the full account of his theory as read at 7 March 1785 and 4 April 1785 meetings did not appear in print until 1788. It was titled Theory of the Earth; or an Investigation of the Laws observable in the Composition, Dissolution, and Restoration of Land upon the Globe and appeared in Transactions of the Royal Society of Edinburgh, vol. I, Part II, pp. 209–304, plates I and II, published 1788. He put forward the view that “from what has actually been, we have data for concluding with regard to that which is to happen thereafter.” This restated the Scottish Enlightenment concept which David Hume had put in 1777 as “all inferences from experience suppose … that the future will resemble the past”, and Charles Lyell memorably rephrased in the 1830s as “the present is the key to the past”. Hutton’s 1788 paper concludes; “The result, therefore, of our present enquiry is, that we find no vestige of a beginning,–no prospect of an end.” His memorably phrased closing statement has long been celebrated. (It was quoted in the 1989 song “No Control” by songwriter and professor Greg Graffin.)

He went on to find a similar penetration of volcanic rock through sedimentary rock in Edinburgh, at Salisbury Crags, adjoining Arthur’s Seat – this area of the Crags is now known as Hutton’s Section. He found other examples in Galloway in 1786, and on the Isle of Arran in 1787.

The existence of angular unconformities had been noted by Nicolas Steno and by French geologists including Horace-Bénédict de Saussure, who interpreted them in terms of Neptunism as “primary formations”. Hutton wanted to examine such formations himself to see “particular marks” of the relationship between the rock layers. On the 1787 trip to the Isle of Arran he found his first example of Hutton’s Unconformity to the north of Newton Point near Lochranza, but the limited view meant that the condition of the underlying strata was not clear enough for him, and he incorrectly thought that the strata were conformable at a depth below the exposed outcrop.

Later in 1787 Hutton noted what is now known as the Hutton or “Great” Unconformity at Inchbonny, Jedburgh, in layers of sedimentary rock. As shown in the illustrations to the right, layers of greywacke in the lower layers of the cliff face are tilted almost vertically, and above an intervening layer of conglomerate lie horizontal layers of Old Red Sandstone. He later wrote of how he “rejoiced at my good fortune in stumbling upon an object so interesting in the natural history of the earth, and which I had been long looking for in vain.” That year, he found the same sequence in Teviotdale.

From 1791 Hutton suffered extreme pain from stones in the bladder and gave up field work to concentrate on finishing his books. A dangerous and painful operation failed to resolve his illness. He died in Edinburgh and was buried in the vault of Andrew Balfour, opposite the vault of his friend Joseph Black, in the now sealed south-west section of Greyfriars Kirkyard commonly known as the Covenanter’s Prison.

The whole was entitled An Investigation of the Principles of Knowledge and of the Progress of Reason, from Sense to Science and Philosophy when the third volume was completed in 1794. Its 2,138 pages prompted Playfair to remark that “The great size of the book, and the obscurity which may justly be objected to many parts of it, have probably prevented it from being received as it deserves.”

Following criticism, especially the arguments from Richard Kirwan who thought Hutton’s ideas were atheistic and not logical, Hutton published a two volume version of his theory in 1795, consisting of the 1788 version of his theory (with slight additions) along with a lot of material drawn from shorter papers Hutton already had to hand on various subjects such as the origin of granite. It included a review of alternative theories, such as those of Thomas Burnet and Georges-Louis Leclerc, Comte de Buffon.

It has been claimed that the prose of Principles of Knowledge was so obscure that it also impeded the acceptance of Hutton’s geological theories. Restatements of his geological ideas (though not his thoughts on evolution) by John Playfair in 1802 and then Charles Lyell in the 1830s popularised the concept of an infinitely repeating cycle, though Lyell tended to dismiss Hutton’s views as giving too much credence to catastrophic changes.

Though he saw his “principle of variation” as explaining the development of varieties, Hutton rejected the idea that evolution might originate species as a “romantic fantasy”, according to palaeoclimatologist Paul Pearson. Influenced by deism, Hutton thought the mechanism allowed species to form varieties better adapted to particular conditions and provided evidence of benevolent design in nature. Studies of Charles Darwin’s notebooks have shown that Darwin arrived separately at the idea of natural selection which he set out in his 1859 book On the Origin of Species, but it has been speculated that he had some half-forgotten memory from his time as a student in Edinburgh of ideas of selection in nature as set out by Hutton, and by William Charles Wells and Patrick Matthew who had both been associated with the city before publishing their ideas on the topic early in the 19th century.