The Sentinel ran aground in St. Helena Sound almost immediately, leaving only the Harriet A. Weed and the John Adams to continue. Around three o'clock in the morning of June 2, the two ships reached the mouth of the Combahee at Fields Point. Montgomery landed a detachment that drove off Confederate pickets, and the small fleet pushed upriver. The timing was deliberate: summer in the Lowcountry brought malaria, typhoid, and smallpox, and Confederate commanders had pulled most of their troops back from the swampy riverbanks, leaving only skeleton detachments. A recent false alarm had made the remaining outposts cautious about responding. By the time the Confederates confirmed the ships were Union, it was too late.

As the John Adams steamed upriver toward Combahee Ferry, mounted Confederates fled across a pontoon bridge. Union troops set the bridge ablaze, then fanned out along both banks. Captain Brayton marched to the Middleton plantation with orders to confiscate everything of value and destroy the rest. Montgomery's soldiers torched William Cruger Heyward's plantation, C.T. Lowndes's rice mill, and the Nichols Plantation. They seized stores of rice, cotton, potatoes, corn, and livestock. By the time Confederate reinforcements arrived from McPhearsonville, Pocotaligo, Green Pond, and Adams Run, they found the Union forces already withdrawing under the covering guns of the John Adams. Outgunned and outnumbered, the Southern troops retreated.

The enslaved people working the rice fields had never heard of the Emancipation Proclamation. When they first spotted the Union ships, they were wary. But word spread fast. Within hours, hundreds of men, women, and children ran for the riverbank, desperate to board. The small boats could not carry them all at once. People clung to the gunwales so tightly that oarsmen could not push off, the boats in danger of capsizing under the weight of freedom. Tubman later recalled the chaos with a single complaint: the excited freedmen had torn her green dress. The boats made trip after trip. By the time the ships turned back toward Beaufort, more than 750 enslaved people had been liberated. Many of the men immediately enlisted in the Union Army.

The Combahee Ferry raid demonstrated two things the Union needed to believe. First, that Black soldiers could fight effectively in combat -- a question that prejudice had kept open despite all evidence. Second, that Harriet Tubman was not merely a symbol of resistance but a military strategist of genuine capability, the first woman to plan and lead an armed military operation in American history. The raid's tactics were adopted for similar operations up and down the coast. The abandoned plantations around Combahee Ferry were never rebuilt during the war, and many of the planters were bankrupted. In 2006, South Carolina named the new US-17 bridge over the Combahee River after Tubman. A statue of her was dedicated in Beaufort on June 1, 2024, the anniversary of the night the ships went upriver.