On 16 June 1809 "Agamemnon", along with the rest of the squadron (which was now under the command of Rear-Admiral Michael de Courcy), put into Maldonado Bay for the third and final time, to shelter from a storm. While working her way between Gorriti Island and the shore, "Agamemnon" struck an uncharted shoal. Captain Jonas Rose attempted to use the ship's boats, together with the stream and kedge anchors, to pull the ship off, but to no avail. The ship had dropped anchor on the shoal just previously, and it was discovered that she had run onto it when she grounded, the anchor having pierced the hull. On 17 June, with the ship listing heavily to starboard, "Agamemnon"s stores and all her crew were taken off by boats from other vessels in the squadron, and the following day Captain Rose and his officers left the ship.