His father, William Cotton (1627–1674), notable Iron-master of Wortley Top Forge, was and Dissenter, noted for his great hospitality and kindness to the ejected ministers.
One of these was a John Spawford, ejected from Silkstone in 1662, whom he received into his family as tutor to his son until his death in 1668.
He then accepted a position as tutor and governor to a young gentleman, and spent three years touring Europe, during which he witnessed the ejection of Protestant ministers at Loudun, Poitou and Saumur, which he later described in the unpublished memoirs of his travels.
He settled first at Hoxton Square, London (1690–95), then Ware in Hertfordshire (1695–99), finally at Dyot Street Chapel, St. Giles’s in the Fields, Bloomsbury (1699–1727).
In 1689, he married Bridget Hoar, with whom he had three children: Leonard (1693–1770; who emigrated to America); Thomas (1710–97), and Alicia (b.