At Glen Tilt in the Cairngorm mountains in the Scottish Highlands, Hutton found granite penetrating metamorphic schists, in a way which indicated that the granite had been molten at the time. This showed to him that granite formed from cooling of molten rock, not precipitation out of water, and that the granite must be younger than the schists.

Hutton's Section Plaque, Salisbury Crags, Edinburgh. Placed by Historic Scotland.He also noted what became known as "Hutton's Unconformity" in layers of sedimentary rocks at Siccar Point on the Berwickshire coast (Grid reference NT813710) about midway between Dunbar and Eyemouth, some 30 miles (50 km) east of Edinburgh. Here, the lower part of the cliff shows layers of grey shale tilted to lie almost vertically, then immediately above this the upper part of the cliff shows near horizontal layers of red sandstone.

Hutton reasoned that there must have been several cycles, each involving deposition on the seabed, uplift with tilting and erosion then undersea again for further layers to be deposited, and there could have been many cycles before over an extremely long history. At Siccar Point around 1786 he remarked of this discovery of geological time "that we find no vestige of a beginning, no prospect of an end", and when he brought John Playfair to see the strata, Playfair commented that "the mind seemed to grow giddy by looking so far into the abyss of time".

Publication
An abstract of Hutton's Theory was first read at meetings of the Royal Society of Edinburgh on 7 March 1785 and 4 April 1785. It was then published in Volume I of the Transactions of the Royal Society of Edinburgh, 1788.

Following criticism, especially that of Richard Kirwan, who accused him of atheism and poor logic, among other things, Hutton published a two volume version of his theory in 1795, consisting of the 1788 version of his theory (with slight additions) along with much material drawn from shorter papers Hutton already had to hand on various subjects, such as the origin of granite. It also included a review of alternative theories, such as those of Thomas Burnet and Georges-Louis Leclerc, Comte de Buffon. A third volume was never completed.

Its 2,138 pages of opaque prose made Playfair 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."

Opposing theories
His new theories placed him into opposition with the then-popular Neptunist theories of Abraham Gottlob Werner, that all rocks had precipitated out of a single enormous flood. Hutton proposed that the interior of the Earth was hot, and that this heat was the engine which drove the creation of new rock: land was eroded by air and water and deposited as layers in the sea; heat then consolidated the sediment into stone, and uplifted it into new lands. This theory was dubbed "Plutonist" in contrast to the flood-oriented theory.

As well as combatting the Neptunists, he also opened up the concept of deep time for scientific purposes, in opposition to Catastrophism. Rather than accepting that the earth was no more than a few thousand years old, he maintained that the Earth must be much older (indeed, he went rather overboard and asserted that the Earth was infinitely old). His main line of argument was that the tremendous displacements and changes he was seeing did not happen in a short period of time by means of catastrophe, but that processes still happening on the Earth in the present day had caused them.

As these processes were very gradual, the Earth needed to be ancient, in order to allow time for the changes. Before long, scientific inquiries provoked by his claims had pushed back the age of the earth into the millions of years – still too short when compared with what is known in the 21st century, but a distinct improvement.

Acceptance of geological theories
The prose of Principles of Knowledge was so obscure, in fact, 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 removed this hinderance. If anything, Hutton's ideas were eventually accepted too well. At least some of the initial resistance to modern scientific ideas like plate tectonics and asteroid strikes causing mass extinctions can be attributed to too-strict adherence to uniformitarianism.

Other contributions

Meteorology
It was not merely the earth to which Hutton directed his attention. He had long studied the changes of the atmosphere. The same volume in which his Theory of the Earth appeared contained also a Theory of Rain. He contended that the amount of moisture which the air can retain in solution increases with temperature, and, therefore, that on the mixture of two masses of air of different temperatures a portion of the moisture must be condensed and appear in visible form. He investigated the available data regarding rainfall and climate in different regions of the globe, and came to the conclusion that the rainfall is regulated by the humidity of the air on the one hand, and mixing of different air currents in the higher atmosphere on the other.

Evolution
Hutton also advocated uniformitarianism for living creatures too – evolution, in a sense – and even suggested natural selection as a possible mechanism affecting them:

"...if an organised body is not in the situation and circumstances best adapted to its sustenance and propagation, then, in conceiving an indefinite variety among the individuals of that species, we must be assured, that, on the one hand, those which depart most from the best adapted constitution, will be the most liable to perish, while, on the other hand, those organised bodies, which most approach to the best constitution for the present circumstances, will be best adapted to continue, in preserving themselves and multiplying the individuals of their race." – Investigation of the Principles of Knowledge, volume 2
Hutton gave the example that where dogs survived through "swiftness of foot and quickness of sight... the most defective in respect of those necessary qualities, would be the most subject to perish, and that those who employed them in greatest perfection... would be those who would remain, to preserve themselves, and to continue the race". Equally, if an acute sense of smell was "more necessary to the sustenance of the animal... the same principle [would] change the qualities of the animal, and.. produce a race of well scented hounds, instead of those who catch their prey by swiftness". The same "principle of variation" would influence "every species of plant, whether growing in a forest or a meadow".

He came to his ideas as the result of experiments in plant and animal breeding, some of which he outlined in an unpublished manuscript, the Elements of Agriculture. He distinguished between heritable variation as the result of breeding, and non-heritable variations caused by environmental differences such as soil and climate.

Hutton saw his "principle of variation" as explaining the development of varieties, but rejected the idea of evolution originating species as a "romantic fantasy". As a deist, to him this mechanism allowed species to form varieties better adapted to particular conditions and was evidence of benevolent design in nature. Hutton's ideas on geology were clarified in Charles Lyell's books which Charles Darwin read with enthusiasm during the voyage of the Beagle, and it remained to Darwin to independently develop the idea of natural selection to explain The Origin of Species and bring it to the forefront of public consciousness at the same time as providing the voluminous evidence necessary to win over the scientific community to the theory.