Clayton was born near Preston, in Lancaster County, England, in 1656 or 1657, and was the son of Robert Clayton and Elianor Atherton Clayton. He was distantly related to John Clayton (ca. 1666–1737), who later became Virginia’s attorney general. On July 17, 1674, at age seventeen Clayton matriculated at the University of Oxford’s Saint Alban Hall. Later he transferred to Merton College, where he received a B.A. in January 1678 and an M.A. in 1682. On an unrecorded date he was ordained to the priesthood in the Church of England.
Like many other clergymen, including John Banister (ca. 1650–1692), who was in Virginia when Clayton arrived, Clayton had a keen interest in the natural sciences and is known at least as much for his scientific experiments and observations as for his career in the church. He experimented with a “digester,” a precursor to the pressure cooker, studied the weights of liquids, and is credited by some authors with discovering gas lighting no later than 1687. Clayton recorded his observations of numerous natural phenomena, including subjects as diverse as the anatomy of English fowl and Virginia’s animals, geology, native peoples, plants, and weather. He presented accounts of his observations to the Royal Society of London for Improving Natural Knowledge, of which he was elected a fellow on November 30, 1688.
Clayton traveled to Virginia early in 1684 to become rector of James City Parish in Jamestown, a posting that afforded him an opportunity to serve the church and further his scientific pastime in a part of the world few European scientists had the occasion to visit. He collected numerous bird specimens, built a distillery and tried his hand at distilling various native plants, asserted he had discovered hundreds of herbs then unknown in Europe, made detailed investigations of the colony’s flora and fauna, and answered a long questionnaire on the colony’s natural life for Sir Robert Boyle. So thorough and impressive were Clayton’s accounts of Virginia that John Brickell plagiarized his works for his own Natural History of North-Carolina (1737). Clayton made perceptive observations of the colony’s settlers as well. One valuable document that he acquired was the journal that Thomas Batte and Robert Hallom kept on an exploratory march to the New River and beyond the Appalachian Mountains in 1671. Misspellings of the principals’ surnames in the copy that Clayton presented in 1688 to the Royal Society in London led to their later misidentification in published accounts as Batts and Fallam. Clayton doubtless would have engaged in other serious scientific investigations while in Virginia had the vessel on which he shipped his reference books and scientific instruments to the colony not been lost at sea.
Clayton’s reputation as a preacher preceded him to Virginia. Shortly after arriving he received an invitation from the governor and Council to preach to the General Assembly. He joked: “I must mind my hits to preserve that blooming repute I have got. I have had the happinesse to be cried up farr beyond my deserts.” Clayton’s learned sermons, full of references to the church fathers and church history and buttressed with numerous Latin footnotes, probably appealed to the better-educated Virginians, among whom he made friends, however members of the assembly received them.
When Clayton was in Virginia, Henry Compton was bishop of London and had jurisdiction over the church in the North American colonies. The fortunes of the Church of England, which was the established church in the colony, were looking up. Until then, the church and the Crown had failed to take an adequate interest in Virginia’s religious life. As a result, many parishes were without ministers, and ministers lacking proper ordination filled some pulpits. The clergy was unsupervised, holy days were not celebrated, and wealthy members of the laity preferred burial in their gardens rather than the churchyard. Among the steps Compton took to improve Virginia’s religious life was to send qualified ministers, such as Clayton, to Virginia parishes. On an unrecorded date, probably not long after Clayton arrived in Virginia, the governor at Compton’s request nominated Clayton to become the colony’s first commissary, or personal representative of the bishop. Although new to the colonies, this administrative position was common in England and provided for the administration of the bishop’s episcopal authority without requiring his formal presence, thus making it the perfect means of establishing the Church of England’s ecclesiastical authority in North America.
As commissary, Clayton took part in the Anglicization of Virginia. He later stated that he had “Setled the Service of our Church very Regularly” and been the first minister in Jamestown to wear a surplice. He took pride in his ability to convert dissenters. In order to help both conformists and dissenters better understand the Church of England’s set liturgies, he offered regular afternoon lectures on the Book of Common Prayer and by this means, as he put it, “brought over many Dissenters to be very affectionate to our Church Service.” Clayton also baptized enslaved blacks and readily accommodated himself to planters’ needs by helping “to take off one grand Obstruction that had Obtain’d, Viz. a Notion, that Negroes being Baptiz’d were immediately Free.”
Clayton left Virginia in May 1686, and consequently his leadership as commissary may have left little mark on the colony’s established church. After returning to England, he became rector of the Church of All Saints in Crofton, Yorkshire, in 1687 and sometime before the end of 1694 married Juliana Edmundson. They had three daughters and two sons, one of whom became a bishop. In 1697 Clayton accepted the position of rector at Saint Michan’s Church, in Dublin, and moved to Ireland at a time when relations between Catholics and Protestants remained tense. His three extant published sermons contain elements of anti-Catholic polemic. In the preface to a 1701 discourse he described his ministry in Virginia. John Clayton was elected dean of Kildare in 1708, in which office he was still serving when he died in Dublin on September 23, 1725. He was buried three days later in Saint Michan’s Church in that city.