The lack of trained artillerymen meant that Arnold could never match the weight and number (148) of Carleton's guns, but even so the governor took no chances. When a foraging party found recently manufactured scaling ladders outside the St Louis Bastion, he ordered the snow drifts cleared from the ditch, barricaded the Lower Town with blocks of ice from the river, built two blockhouses outside the walls, and cut a trench in the river ice under Cape Diamond to prevent the picket barriers being outflanked. At night, fireballs lit the darker recesses of the ditch. But the attack never came.
Although no attack came from the outside, the prisoners inside the city were active. The officers in the upper floor of the Seminary, and the enlisted men housed in the Recollet Monastery, and later the Dauphine Bastion, prepared to escape, but both attempts were thwarted. However, some did find a way out. The Royal Highland Emigrants had recruited 94 men from among the British-born prisoners, who were guilty of treason and therefore liable to hang. Within days, 14 of them had gone over the wall (literally) and Carleton had the rest disarmed. Otherwise, American activity was reduced to indiscriminate shelling of the Upper and Lower Towns - an act condemned by many of the captured officers watching the bombardment from the windows of the Seminary.
On 1 May, Major General John Thomas of Massachusetts replaced Wooster, bringing with him over 1,200 men. On the night of 3 May, with the river now open, a brig was spotted moving upriver. However, when it failed to answer the identification signals Carleton had agreed with Pringle before his departure, the guns in the Lower Town pounded the vessel. Men were seen fleeing in a small boat: the brig was a fireship designed to destroy the shipping at Queen's Wharf. It was also the swansong of the American forces besieging Quebec.
Concerned at the state of the army, Thomas had proposed to withdraw to Jacques Carrier and Deschambault and fortify those places. Unfortunately, the following day saw the arrival of the first British ships - the frigate Surprise closely followed by the ship Isis and the sloop Martin. From them disembarked 200 men of the 29th Foot and Marines. Learning that Thomas was pulling back, Carleton immediately ordered a sortie. Adding the 7th Foot, Royal Highland Emigrants, and city militia to the fresh troops, he attacked Thomas's encampment with 900 men and turned the latter's orderly withdrawal into a panic-stricken retreat.
By 7 May the exhausted Americans - many with smallpox - had halted in Deschambault, where they were shelled by British vessels on the St Lawrence. Thomas wanted to make a stand but his army did not. The men were tired and sick and the position could easily be taken in the rear by Carleton, who had complete command of the river. Thomas ordered his troops back to Sorel, leaving 500 men to garrison Deschambault, but even these were withdrawn several days later.
