On the night of the 16th, after the defeat at Champion Hill, Pemberton formed a line at the crossing of the Big Black River in order to buy time for his army. For this rear guard, Pemberton selected the Missouri troops of Bowen's division, Brigadier General John C. Vaughn's Tennessee brigade, and the 4th Mississippi Infantry Regiment. This force numbered about 5,000 men. The left of the Confederate line was held by Brigadier General Martin E. Green's brigade of Bowen's division, Vaughn's brigade held the center, Bowen's other brigade, commanded by Colonel Francis M. Cockrell, was positioned on the Confederate right, and the 4th Mississippi was placed between Cockrell and Vaughn. Vaughn's brigade was composed of inexperienced conscripts, and Bowen's division had seen heavy fighting at Champion Hill. The Confederate line was supported by Wade's Missouri Battery, Landis' Missouri Battery, and Guibor's Missouri Battery. A railroad ran through the Confederate position, and the river could be crossed either over the railroad bridge or over a steamboat that had been positioned crossways across the river, creating a makeshift bridge.
On the morning of May 17, McClernand's XIII Corps advanced towards the Confederate position at the Big Black River. Brigadier General Eugene A. Carr's division led the way, and deployed to confront the Confederate lines. The brigade of Brigadier General Michael K. Lawler formed the right of the Union line. Carr was soon reinforced by Brigadier General Peter J. Osterhaus' division. An artillery duel began, and Osterhaus was wounded in the leg by a shell fragment. After some preparations, Lawler's brigade charged, quickly breaking the Confederate line. Vaughn's brigade routed to the rear, and the gap in the line quickly forced Green's brigade to retreat as well. Lawler's charge had lasted only three minutes. Cockrell's brigade also collapsed in much disorder, one survivor summarized the retreat as "the devil take the hindmost being the order of the day." The 1st and 4th Missouri Infantry Regiment (Consolidated) served as a rear guard for the retreating Confederates, as it was one of the few units still in functioning order. The Confederates lost a number of cannons in the retreat due to an error; the horses for Wade's Battery, Guibor's Battery, and a portion of Landis's Battery had been positioned on the far side of the Big Black River, and were not available to haul off the cannons. In total, the Confederates lost 18 cannons at the Big Black River. The retreating Confederates burned both the bridge and the steamboat serving as a bridge, and those who escaped the Union army joined the fortifications at Vicksburg.
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Sergeant William Wesley Kendall of the 49th Indiana Infantry Regiment was awarded the Medal of Honor for leading a company in the main Union charge; he was among the first Union soldiers to enter the Confederate fortifications.