Cotton was married in Balsham, Cambridgeshire, on 3 July 1613 to Elizabeth Horrocks, but this marriage produced no children.
 Elizabeth died about 1630.
Cotton married Sarah, the daughter of Anthony Hawkred and widow of Roland Story, in Boston, Lincolnshire, on 25 April 1632, and they had six children.
 His oldest child Seaborn was born during the crossing of the Atlantic on 12 August 1633, and he married Dorothy, the daughter of Simon and Anne Bradstreet.
 Daughter Sariah was born in Boston (Massachusetts) on 12 September 1635 and died there in January 1650.
 Elizabeth was born 9 December 1637, and she married Jeremiah Eggington.
John was born 15 March 1640; he attended Harvard and married Joanna Rossiter.
 Maria was born 16 February 1642 and married Increase Mather, the son of Richard Mather.
 The youngest child was Rowland, who was baptized in Boston on 24 December 1643 and died in January 1650 during a smallpox epidemic, like his older sister Sariah.

Following Cotton's death, his widow married the Reverend Richard Mather.
 Cotton's grandson, Cotton Mather who was named for him, became a noted minister and historian.
 Among Cotton's descendants are U.S. Supreme Court Justice Oliver Wendell Holmes Jr., Attorney General Elliot Richardson, actor John Lithgow, and clergyman Phillips Brooks.
Cotton was married in Balsham, Cambridgeshire, on 3 July 1613 to Elizabeth Horrocks, but this marriage produced no children.  Elizabeth died about 1630. Cotton married Sarah, the daughter of Anthony Hawkred and widow of Roland Story, in Boston, Lincolnshire, on 25 April 1632, and they had six children.  His oldest child Seaborn was born during the crossing of the Atlantic on 12 August 1633, and he married Dorothy, the daughter of Simon and Anne Bradstreet.  Daughter Sariah was born in Boston (Massachusetts) on 12 September 1635 and died there in January 1650.  Elizabeth was born 9 December 1637, and she married Jeremiah Eggington. John was born 15 March 1640; he attended Harvard and married Joanna Rossiter.  Maria was born 16 February 1642 and married Increase Mather, the son of Richard Mather.  The youngest child was Rowland, who was baptized in Boston on 24 December 1643 and died in January 1650 during a smallpox epidemic, like his older sister Sariah.
Following Cotton's death, his widow married the Reverend Richard Mather.  Cotton's grandson, Cotton Mather who was named for him, became a noted minister and historian.  Among Cotton's descendants are U.S. Supreme Court Justice Oliver Wendell Holmes Jr., Attorney General Elliot Richardson, actor John Lithgow, and clergyman Phillips Brooks.
John Cotton (minister)