The new Cole Junction Pump Station is operating, and crews are diverting sewage from the old pipeline that is no longer needed to the new pump station.
As the sewage is being drained from the old pipeline, odors are evident in the area, officials said.
"Unfortunately, we cannot control the odor from the old pipeline that is being drained back to the new pump station," said Eric Seaman, Jefferson City wastewater division director.
Seaman said landscaping work on the pump station site, across from Boonville Road near the railroad crossing on Missouri 179, will have no effect on traffic in that area. He also said the old pump station will be demolished, and that work will run through next week.
The station is the starting point for the city's new sewer pipeline. Work began on the project in December 2012.
The 4 1/2-mile line runs under the Missouri River to the city's sewer treatment plant near the airport.
Seaman said they put the new line into operation Tuesday.
The $12.5 million project is believed to be the largest ever done by the city. It was financed through the state's revolving loan program used for communities with sewer infrastructure needs.