More than 10,000 gallons of wastewater has spilled into the Jones Falls since Wednesday.
The Baltimore City Department of Public Works says the overflow was halted early Friday afternoon.
While it is still trying to determine the cause, DPW says the incident happened underground in a structured overflow at West Garrison Avenue and Queensberry Road. The overflow did not spill onto any streets.
According to DPW, structured overflows were designed into the city's sewer system more than 100 years ago. They act as release valves when the pipes are surcharged with rainwater that enters sewer mains during larger storms.
As part of a $2 billion consent decree to rehabilitate Baltimore's sewer system, the structured overflows are being eliminated.