"We're already working with the owner and a contractor to fix it as quickly as possible," Utilities Director Tom Wiedmeier said.
Workers are using smoke pumped into storm drains as part of an effort to identify the source of elevated levels of fecal coliform bacteria entering the river.
On Wednesday, smoke forced into a storm drain at River Glen apartments appeared in a nearby sewer manhole -- an indicator that sewage was flowing into the storm drain.
The leak was calculated at about 4 gallons per minute -- or 5,760 gallons per day.
Wiedmeier said the leak was at a pipe joint in the manhole, which is part of the building's private sewer system.
He was unsure how long it had leaked, saying, "The joint was probably holding when the system was built, but it wasn't when we tested it."
Fixing the problem is a one- to two-day job and will require replacing a 20-foot section of pipe, he said.
Garrett Weiss, the manager of the city's Stormwater and Environmental Section, said the 4-gallon-per-minute flow is not necessarily pure human waste.
"A nearby car wash may also be contributing to the flow," Weiss said.
Although contaminated water entering the river has high bacteria levels, the small flow does not represent an elevated health threat to swimmers in the river.
"As stated previously, as long as no one swims immediately next to the storm pipe outfall, the exposure risk to coliform is the about the same as in any other natural water body flowing through populated areas with humans, pets, livestock, and wildlife," Weiss said.
To put it in perspective, he added, the storm drain's rate of discharge is less than 10 gallons per minute, compared with a typical flow in the Savannah River of 2 million gallons per minute.
Engineers are continuing to search for the source of elevated bacteria levels at another drain on Second Street.
The contamination came to light as part of a project last month by The Augusta Chronicle. Water samples from 50 locations were analyzed for a story on water quality and bacteriological monitoring.