The son of hand-loom weaver from Eaglesfield in the northwestern English county of Cumbria, Dalton was born into the nonconformist tradition of the region and remained a Quaker all his life. He was educated at the village school until the age of 11, and received tuition from Elihu Robinson, a wealthy Quaker, meteorologist, and instrument maker, who first encouraged Dalton's interest in meteorology. At the age of only 12, Dalton himself was teaching in the village. He then worked on the land for two years before moving to Kendal with his brother to teach (1781). In 1793 he moved to Manchester where he first taught at the Manchester New College, a Presbyterian institute. In 1794 he was elected to the Manchester Literary and Philosophical Society at which most of his papers were read.

From 1787 until his death Dalton maintained a diary of meteorological observations of the Lake District where he lived. His first published work, Meteorological Observations and Essays (1793), contained the first of his laws concerning the behavior of compound atmospheres: that the same weight of water vapor is taken up by a given space in air and in a vacuum. Both Dalton and his brother were color blind and he was the first to describe the condition, sometimes known as daltonism, in his work Extraordinary Facts Relating to the Vision of Colours (1794).

In 1801 Dalton read four important papers to the Manchester Philosophical Society. On the Constitution of Mixed Gases contains what is now known as the law of partial pressures and asserts that air is a mixture, not a compound, in which the various gases exert pressure on the walls of a vessel independently of each other. On the Force of Steam includes the first explanation of the dew point and hence the founding of exact hygrometry. It also demonstrates that water vapor behaves like any other gas. The third paper, On Evaporation, shows that the quantity of water evaporated is proportional to the vapor pressure. On the Expansion of Gases by Heat contains the important conclusion that all gases expand equally by heat. This law had been discovered by Jacques Charles in 1787 but Dalton was the first to publish.

During this time, Dalton was developing his atomic theory, for which he is best known. A physical clue to the theory was provided by the solubility of gases in water. Dalton expected to find that all gases had the same solubility in water but the fact that they did not helped to confirm his idea that the atoms of different gases had different weights. The first table of atomic weights was appended to the paper On the Absorption of Gases by Water read in 1802 but not printed until 1805. In another paper read in 1802 and printed in 1805 he showed that when nitric oxide is used to absorb oxygen in a eudiometer they combine in two definite ratios depending on the method of mixing. This was the beginning of the law of multiple proportions and led Dalton to much work on the oxides of nitrogen and the hydrocarbons methane and ethylene to confirm the law.

The atomic theory was first explicitly stated by Dalton at a Royal Institution lecture in December 1803 and first appeared in print in Thomas Thomson's System of Chemistry (1807). Dalton's own full exposition appeared in A New System of Chemical Philosophy (1808), with further volumes in 1810 and 1827. The basic postulates of the theory are that matter consists of atoms; that atoms can neither be created nor destroyed; that all atoms of the same element are identical, and different elements have different types of atoms; that chemical reactions take place by a rearrangement of atoms; and that compounds consist of ‘compound atoms’ formed from atoms of the constituent elements.

Using this theory, Dalton was able to rationalize the various laws of chemical combination (conservation of mass, definite proportions, multiple proportions) and show how they followed from the theory. He did, however, make the mistake of assuming “greatest simplicity”: i.e. that the simplest compound of two elements must be binary (e.g. water was HO). His system of atomic weights was not very accurate (e.g. he gave oxygen an atomic weight of seven rather than eight). Dalton's theory remained open to dispute until 1858 when Stanislao Cannizzaro's rediscovery of Amedeo Avogadro's work removed the last objections to the theory. Dalton's symbols for atoms and molecules were spherical representations and he used wooden molecular models similar to the modern version.