Near the town of Sharpsburg, Lee deployed his available forces behind Antietam Creek along a low ridge, starting on September 15. While it was an effective defensive position, it was not an impregnable one. The terrain provided excellent cover for infantrymen, with rail and stone fences, outcroppings of limestone, little hollows and swales. The creek to their front was only a minor barrier, ranging from 60 to 100 feet (18–30 m) in width, and was fordable in places and crossed by three stone bridges each a mile (1.5 km) apart. It was also a precarious position because the Confederate rear was blocked by the Potomac River and only a single crossing point, Boteler's Ford at Shepherdstown, was nearby should retreat be necessary. (The ford at Williamsport, Maryland, was 10 miles (16 km) northwest from Sharpsburg and had been used by Jackson in his march to Harpers Ferry. The disposition of Union forces during the battle made it impractical to consider retreating in that direction.) And on September 15, the force under Lee's immediate command consisted of no more than 18,000 men, only a third the size of the Federal army.^[7]

The first two Union divisions arrived on the afternoon of September 15 and the bulk of the remainder of the army late that evening. Although an immediate Union attack on the morning of September 16 would have had an overwhelming advantage in numbers, McClellan's trademark caution and his belief that Lee had as many as 100,000 men at Sharpsburg caused him to delay his attack for a day.^[8] This gave the Confederates more time to prepare defensive positions and allowed Longstreet's corps to arrive from Hagerstown and Jackson's corps, minus A.P. Hill's division, to arrive from Harpers Ferry. Jackson defended the left (northern) flank, anchored on the Potomac, Longstreet the right (southern) flank, anchored on the Antietam, a line that was about 4 miles (6 km) long. (As the battle progressed and Lee shifted units, these corps boundaries overlapped considerably.)^[9]

On the evening of September 16, McClellan ordered Hooker's I Corps to cross Antietam Creek and probe the enemy positions. Meade's division cautiously attacked Hood's troops near the East Woods. After darkness fell, artillery fire continued as McClellan positioned his troops for the next day's fighting. McClellan's plan was to overwhelm the enemy's left flank. He arrived at this decision because of the configuration of bridges over the Antietam. The lower bridge (which would soon be named Burnside Bridge) was dominated by Confederate positions on the bluffs overlooking it. The middle bridge, on the road from Boonsboro, was subject to artillery fire from the heights near Sharpsburg. But the upper bridge was 2 miles (3 km) east of the Confederate guns and could be crossed safely. McClellan planned to commit more than half his army to the assault, starting with two corps, supported by a third, and if necessary a fourth. He intended to launch a simultaneous diversionary attack against the Confederate right with a fifth corps, and he was prepared to strike the center with his reserves if either attack succeeded.^[10] The skirmish in the East Woods served to signal McClellan's intentions to Lee, who prepared his defenses accordingly. He shifted men to his left flank and sent urgent messages to his two commanders who had not yet arrived on the battlefield: Lafayette McLaws with two divisions and A.P. Hill with one division.^[11]