The State newspaper reported the Department of Health and Environmental Control has warned against fishing or kayaking in the area north of downtown Columbia.
DHEC spokesman Adam Myrick says a spill Sunday morning and another Monday morning leaked sewage into the river.
Myrick says repairs are being made at Broad River Correctional Institution.
The Department of Corrections says the overflow began about 11 a.m. Sunday after a sewer pump failure. Myrick says the station had another problem Monday morning.