The current governor Alexander Campbell was a "careful and good man", but there were doubts about his competence; on 15 March 1746, he was replaced by Captain Caroline Frederick Scott of Guise's Regiment.

A well-built, modern position, its triangular shape was designed to use the head of Loch Linnhe as cover; it had six 12-pounder cannon, eight 6-pounders, seven smaller pieces, two 13-inch mortars and eight coehorns, with plenty of ammunition.

Additional firepower was provided by the sloop of war Baltimore and the Serpent, a bomb vessel; this made it a formidable target, its only weakness being lack of a permanent water supply.

[6] On 25 February 1746, the garrison began demolishing buildings in the nearby village of Maryburgh to provide a clear field of fire, although they could not prevent the besiegers occupying the surrounding heights.

[6] Campbell militia under Argyll destroyed property and livestock in the surrounding area, denying supplies to the Jacobites but also putting pressure on Cameron and MacDonald clansmen to defend their lands.

[citation needed] Charles and his senior Scots commander Lord George Murray agreed with Stapleton but Lochiel and Keppoch insisted, due to the damage caused to their lands by the garrison.

Although the 6-inch guns apparently caused some concern, Scott's counter-battery fire proved effective; clear, moonlit nights prevented the Jacobites getting close without being seen and the only opportunity for combat was when water parties left the fort.

[6] In the aftermath of the siege, the Baltimore and Terror were employed intercepting French supply ships and preventing clansmen in the Western Highlands and Islands reinforcing the main Jacobite army.

[6] In the repression that followed Culloden, Scott conducted the search for Prince Charles, gaining a reputation for brutality; most of the stories lack witnesses but he appears to have actively disliked Highlanders.