Saussure was the son of an agriculturist. He was educated at the university in his native city of Geneva, graduating in 1759, and became professor of physics and philosophy at the Geneva Academy (1762–86).

He was the first to make a systematic and prolonged study of the Alps, his work being published in his classic Voyages dans les Alpes (1779–96; Travels in the Alps). He began as a disciple of Abraham Werner, accepting that the mass of the Alps had crystallized from the primitive ocean. However, 17 years of studying the convolutions and folds of the Alps led him to state in 1796 that such folds could only be produced by some force acting from below, or that they must have actually been laid down folded. Both alternatives preclude deposition by water. He was unwilling to decide in favor of the plutonist theories of James Hutton and thus to introduce fire as an agent, for he could recognize no sign of it.

He also collected considerable meteorological data and developed, in 1783, an improved hygrometer to measure humidity, using a human hair. He made the second ascent of Mont Blanc (1787) and at the summit took many scientific recordings. He also made nocturnal recordings and, in 1788, stayed for 17 days on the 11,000-foot (3358 m) summit of Col du Géant.