Roof's attorney, public defender Ashley Pennington, said his 21-year-old client was prepared to "accept the no bond arrangement". Judge James Gosnell set the next court hearing in the case for October 23.
Bond was set at $1m on a weapons charge, but Roof will nevertheless remain in custody because no bond was set on the murder charges.
Roof appeared in court via videolink and was seen standing quietly through the hearing, providing brief answers to the judge's questions.
Investigators say he has told them he wanted the shootings to spark a race war in the US.
Early on Friday, Roof was charged with nine counts of murder and one count of possession of a firearm.
The charges came hours after he confessed to carrying out the attack.
US officials are investigating the attack, in which four ministers were killed including a Democratic state senator, as a hate crime.
The justice department announced on Friday that it's investigating whether it could be a hate crime or domestic terrorism, Al Jazeera reported.