Serving as a political advisor to the prominent statesman James Douglas, 2nd Duke of Queensberry, Murray assisted him in passing the 1707 Union with England Act through a divided Parliament of Scotland.

In June 1704, due to the "Scotch plot", an unsuccessful attempt by the Duke of Queensberry to incriminate his political rivals, Murray temporarily stepped down as Lord Clerk Register and was replaced by James Johnston.

He soon returned to power and once again assumed the office on 7 April 1705, continuing to serve as a political advisor to the Duke of Queensberry until dying while staying at the village of Inch, Wigtownshire in 1708.

[2] Murray, who had assumed the role of Sheriff of Selkirk in 1675, became involved in a dispute with Scots Army officer John Urquhart of Meldrum on 18 November 1680 over issues of legal jurisdiction between the two parties.

[2] The Privy Council of Scotland heard the case in January 1681, and issued a ruling on 6 October 1681 which stipulated that Murray was to be immediately removed from his position as sheriff because he had "malversed and been remiss in punishing conventicles.

"[2][3][4][b] In September 1684, Murray was arrested and imprisoned following the discovery of the Rye House Plot, a secret conspiracy to assassinate the Stuart King Charles II and his brother (and heir apparent) James, Duke of York.

[2] In spite of distaste in Scotland towards Murray due to his testimony, after the Glorious Revolution of 1688, which saw William of Orange overthrow the House of Stuart and assume control over the English throne, his fortunes began to recover.

In 1700, Murray encouraged Queensberry to grant several concessions to the Parliament of Scotland over the disastrous failure of the Darien scheme, which had bankrupted much of the Scottish aristocracy and caused widespread discontent and anger.

Murray was temporarily replaced in the office of Lord Clerk Register by James Johnston, and the Duke of Queensberry also briefly stepped back from the Scottish political scene.

[2][12] Murray returned to power on 7 April 1705, and once again assumed control of the office of Lord Clerk Register, where he assisted Queensberry in successfully passing the 1707 Union with England Act through a divided Scottish Parliament.

The joint-stock company was founded to monopolise Scotland's overseas trade with Africa, India and the West Indies, and was also responsible for the failure of the Darien scheme.

[2] Murray's first son, John, also chose to pursue a career in politics as well, representing the constituencies of Lanark Burghs and Selkirkshire in the Parliament of Great Britain from 1725 until 1747.