He was the second son of George Hay, 2nd Earl of Kinnoull and Ann Douglas, daughter of William Douglas, 7th Earl of Morton. His date of birth is not recorded, but his parents married in 1622 and his youngest brother, Peter, was baptized 11 June 1632. His older brother, George, became the third earl in 1644 after the death of their father. Like his brother, William was a supporter of Charles I and joined forces with James Graham, 1st Marquess of Montrose. Montrose's nephew, Archibald Napier, 2nd Lord Napier, wrote his uncle from Brussels, 14 June 1648, "At my parting from France there went in my company above fifty men that did belong to my Lord Montrose; amongst which was Monsieur Hay, Kinnoull's brother, and severall others of good quality." He inherited the earldom after his older brother died without issue in late 1649 or early 1650. The third earl's date of death is uncertain, but writings referring to the Earl of Kinnoull in early 1650 are believed to be about William. He is mentioned in March 1650 as having arrived in Orkney with a fresh supply of continental troops for the Royalist cause. Charles Gordon, 1st Earl of Aboyne writes that Kinnoull accompanied Montrose after his defeat at the Battle of Carbisdale in April 1650, when he was ultimately captured. Gordon writes that Kinnoull "being faint for lack of meat, and not able to go any further, was left there among the mountains, where it was supposed he perished." Kinnoull in fact escaped death and continued to fight Montrose's cause after the latter's execution in May 1650. In December 1653, he was captured near Glamis and taken prisoner in Edinburgh Castle. Along with some others, the earl succeeded in escaping in May 1654. He joined forces with James Graham, 2nd Marquess of Montrose, being with him in battle at the Wood of Methven in June 1654. On 23 November, Kinnoull was again captured and taken prisoner in Edinburgh Castle, from which he again escaped. Upon the death of his cousin James Hay, 2nd Earl of Carlisle in 1660, Kinnoull succeeded him in the proprietorship of Barbados, but sold it to the Crown in 1661 for a pension. He married first Lady Mary Brudenell, daughter of Robert Brudenell, 2nd Earl of Cardigan. She was born 7 January 1636, in Northampton, and died in 1665. He married secondly, Lady Catherine Cecil, daughter of Charles Cecil, Viscount Cranborne. They had two sons, both of whom succeeded in the earldom:
