Cotton was the eldest son of MP, John Cotton of Landwade, Cambridgeshire, Sheriff of Cambridgeshire and Huntingdonshire in 1549/50.
He was appointed a Justice of the Peace for Cambridgeshire in 1582, served as Custos Rotulorum of Cambridgeshire from 1600 to 1621 (except for 1617) and custos rotulorum of the Isle of Ely from 1601.
He married three times: firstly Elizabeth, the daughter of Thomas Caryll of Warnham, Sussex, secondly Elizabeth, the daughter of Sir Humphrey Bradbourne of Derbyshire and thirdly Anne, the daughter of Sir Richard Hoghton, 1st Baronet of Hoghton Tower and the granddaughter of Sir Richard Houghton, Steward of Amounderness.
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