The senior officers including Maj. General Benjamin Lincoln eventually were exchanged for British officers in American hands. For all others in the Continental army, a long stay on prison boats in Charleston Harbor was the result, where sickness and disease would ravage them. The defeat left no Continental Army in the South and the country wide open for British taking. Even before Lincoln surrendered, the Continental Congress had already appointed Maj. General Horatio Gates to replace him.
The British quickly established outposts in a semicircle from Georgetown to Augusta, Georgia, with positions at Camden, Ninety-Six, Cheraw, Rocky Mount and Hanging Rock in between. Parole was offered to back country rebels and many accepted, including Andrew Pickens. Soon after securing Charleston, Lt. General Henry Clinton gave command of the Southern Theatre to Lt. General Charles Cornwallis and on June 5th, he sailed north back to New York.
General Clinton's one order to General Cornwallis before he left, was to maintain possession of Charleston above all else. Cornwallis was not to move into North Carolina if it jeopordized this holding. Clinton also had ordered that all militia and civilians be released from their parole. But in addition, they must take an oath to the Crown and be at ready to serve when called upon by His Majesty's government. This addition angered many of the locals and led to many deserting or ignoring the order and terms of their parole.