It is possible that John was the John Stone marked aged 40 as a passenger on the ship Elizabeth which sailed from London in 1635. He came to America with his two children by his first wife and, it is thought, with his second wife, Ellen or Eleanor, and her seven children by her first marriage.

John is first recorded as living in Salem in 1636 where he kept a ferry until 1639. The ferry ran from Massey's Cove across Bass River to what is now Beverly, MA. In 1636, John was fined under a law against taking excessive wages, "This economic measure (law) being thought necessary in the colony because of the tremendous labour to be performed and the scarcity of hands to perform it." He and his wife were admonished by the Court to "make bigger bread" in 1639. He shared in the land grants of 1636, 1637, and 1639 and was involved in several lawsuits as plaintiff although the particulars and evidence of the lawsuits have been lost. A William Bowdich was fined ten shillings in 1641 for misinforming the court and causing John Stone to be unjustly fined. John was freed from military training in 1650 because of his age and an "infirmity in an arm."

The records show that John and his family moved to Beverly, MA, before 1662 where he sold seven acres of land to William Dodge, with the use and occupation reserved during the life of "Elener my now wife." He was one of the founders, 23 June 1667, of the Beverly church. The last record of him is in 1667 and he died between that date and 1677 when there is a record of his son and his wife being referred to as "John Stone, Sr. and wife Abigail."

John and his first wife, whose name is unknown, had at least two children, both born in England:

• John, Jr., b. ca. 1622 or ca. 1630; m. Abigail Dixey.
• Nathaniel, b. ca. 1632; d. 8 March 1717/8; m. Remember Corning, daughter of Ensign Samuel and Elizabeth Corning of Beverly, MA.

John, Jr. and Abigail lived in Beverly, MA, where they kept an inn from 1673 to 1682. John took the oath of fidelity in 1677 at which time he was called a "seaman." It is recorded that a rally of the militia, under Capt. Dixey, took place at the Stone inn at eight o'clock on the morning of 14 January 1676.

In legal cases in which she testified, Abigail's age was estimated as forty-three in 1678 and about forty in 1679. The evidence in these cases show that she employed two maids, Sarah Riggs and Mary Barrett, and that included in her clothing were "a great handkershief with spots in it, a lace cap with running strings, and a long neck-cloth laced at both ends."

John, Jr. and his wife Abigail (Dixey) Stone had eight children:

• John, b. in Salem, MA, "25: 9: 1654" (25 November 1654); d. unmarried prior to 1703/4.
• Samuel, b. in Salem, MA, "15: 9: 1658" (15 November 1658).
• William, b. in Beverly, MA, 1662; bpt. in Salem 1665; m. Hannah Walley.
• Jonathan, bpt. in Beverly, MA, "10: 3: 1668" (10 May 1668); m. Hannah Herrick.
• Nehemiah, bpt. in Beverly, MA, 29 May 1670; m. Lydia Hart.
• Abigail, b. in Beverly, MA, ca. 1672; d. in Beverly, 1 June 1724, aged fifty-two; m. Capt. Robert Briscoe. Capt. Briscoe was a man of wealth who presented the town of Beverly with a bell in 1712 and the church with a silver communion cup in 1718. The elegance of his house was still remembered a century after his death in 1729. In the middle of the nineteenth century, a street and a school (Briscoe Hall) in Beverly still had his name. Capt. Riscoe married (2) Elizabeth (Leavitt) Dudley and moved to Exeter, NH.
• Israel, bpt. in Beverly, MA, "27: 4: 1675" (27 June 1675); d. before 1703/4.
• Anna, bpt. in Beverly, MA, 21 Dec. 1679; living unmarried in Beverly in 1703/4.

William and his wife Hannah (Walley) Stone had three children, all born in Bristol, RI:

• Hannah, b. 26 March 1687.
• Abigail, b. 9 July 1689; m. Uriah Leonard, Jr.
• William, b. 27 June 1693; m. Mehitable Lane.