Carstares was then committed to the Tower of London; the following year, 1675, he was transferred to Edinburgh Castle. He was believed to be concerned with Sir James Stewart in the authorship of a pamphlet "An Account of Scotland's Grievances by reason of the D. of Lauderdale's Ministrie, humbly tendered to his Sacred Majesty" (1674). John Maitland, 1st Duke of Lauderdale himself got Carstares to admit he had been involved in printing the pamphlet. Lauderdale used the threat of the torture of the boot, which could be employed legally in Scotland; but Carstares was not tortured. In August 1679 he was released, one of the government sops to Scottish opinion after the Battle of Bothwell Bridge. He cannot therefore have been the William Carstares who was the chief prosecution witness at the trial of William Staley (the first of the Popish Plot trials) in November 1678, although that Carstares was also a Scotsman, and like his namesake is said to have acted as an intelligence agent.