It soon became clear that even 50,000 Union soldiers would not be able to effect a complete encirclement of the Confederate defenses. Pemberton's outlook on escape was pessimistic, but there were still roads leading south out of Vicksburg unguarded by Union troops. Grant sought help from Maj. Gen. Henry W. Halleck, the Union general-in-chief. Halleck quickly began to shift Union troops in the West to meet Grant's needs. The first of these reinforcements was a 5,000-man division from the Department of the Missouri under Maj. Gen. Francis J. Herron on June 11. Herron's troops, remnants of the Army of the Frontier, were attached to McPherson's corps and took up position on the far south. Next came a three division detachment from XVI Corps led by Brig. Gen. Cadwallader C. Washburn on June 12, assembled from troops at the nearby posts of Corinth, Memphis, and LaGrange. The final significant group of reinforcements to join was the 8,000-man strong IX Corps from the Department of the Ohio, led by Maj. Gen. John G. Parke, arriving on June 14. With the arrival of Parke, Grant had 77,000 men around Vicksburg.

During the siege, Union gunboats lobbed over 22,000 shells into the town and army artillery fire was even heavier. As the barrages continued, suitable housing in Vicksburg was reduced to a minimum. A ridge, located between the main town and the rebel defense line, provided lodging for the duration. Over 500 caves, known locally as "bombproofs", were dug into the yellow clay hills of Vicksburg. Whether houses were structurally sound or not, it was deemed safer to occupy these dugouts. People did their best to make them comfortable, with rugs, furniture, and pictures. They tried to time their movements and foraging with the rhythm of the cannonade, sometimes unsuccessfully. Because of the citizens' burrowing, the Union soldiers gave the town the nickname of "Prairie Dog Village". Despite the ferocity of the Union fire, fewer than a dozen civilians are known to have been killed during the siege.