John Clay arrived in Virginia in February 1614 aboard the ship, Treasurer. This early arrival date when conditions were more rigorous made him an "ancient planter". His wife, Ann, arrived in August 1623 aboard the Anne. The date of their marriage is not recorded, but probably took place in 1624. They are listed together in the muster of 1625 as living at Jordan's Journey in Charles City.

On 13 July 1635 John Clay patented 1200 acres in Charles City County south of the James River (Prince George County today), together with another 1000 acres a little later. Additional land was patented north of the James near Westover as described in further patents dated in November 1636 and May 1637.  

John and Ann had two sons: William, later a constable of Weyanoke Parish who died without children, and Charles, who appears first in the record as signing on for a seven year apprenticeship in "chyurgery or phissake", i.e. medicine. Charles left four sons and a daughter.

 After Ann's death, date unknown but before 1645, John Clay married a second time - a wife named Elizabeth with whom he had no children.