State officials say the city illegally discharged nine million gallons of partially-treated, un-disinfected effluent into the San Joaquin River.
The action, announced by the California Water Resources Control Board, stems from an incident in 2006 when the discharge occurred.
Board spokeswoman Kathie Smith says the liability assessment by the agency would result in the city becoming more vigilant in its oversight of the treatment plant.
“Our concern always is about water quality. What we want to do is work with them and get their attention. And see that they don't do it again because there are consequences.”
At the time of the violation, the plant was operated by a private company under contract to the city. A spokeswoman says Stockton currently operates the treatment plant and the company that ran the facility at the time of the discharge is going to pay the civil penalty.