ABC 17 News has learned Jefferson City in non-compliant with the Department of Natural Resources.
For the past four years, sewage has been backing up and overflowing every time it rains and now the city must fix the $15 million problem.
The city will spend $11.5 million on a new pump station and a new sewer line. City officials say this project cannot be completed fast enough, but once it is finished, the city will still have other issues that will cause them to be non-compliant with the DNR.
Just within the last week, crews began boring a hole under the Missouri River to install a new sewer line that will be nearly four-and-a-half miles long.
The new line will run from the new Cole Junction pumping station near Boonville Road and Route 179 to the treatment plant across the river from the capitol.
City officials say when it rained, a mixture of rain water and domestic sewage overflowed into creeks.
In 2009, the DNR told the city to fix the problem quickly and the following year, voters approved a $35 million bond issue. DNR is buying those bonds at a bargain rate of two percent per year for 20 years in order to make residents' utility bills hardly change.
City leaders say it took so long because the city had to acquire right of way from levy districts, farmers and the Army Corps of Engineers. They also had to get flood plain permits from both Callaway and Cole counties.
But even after this major upgrade, the city will have a long way to go. The current project will wrap up in January and then the city will have to focus on smaller projects to reach compliance with the DNR.
Those smaller projects are expected to use another $3.5 million of the $35 million approved by voters.