Enrique Zaldivar told the Energy and Environment Committee that his department plans to seek 10 years of rate hikes.
Officials say the rate increases are needed because the department is dramatically underfunded for necessary work on the city's aging sewer system.
They say the system needs to modernized, and the money would be used to fix emergency breaks and prevent major spills.
The city's sewer service rates are at the low end of California municipalities, behind San Francisco, which charges $85 per month, and San Diego, which charges $48 per month, according to a Bureau of Sanitation report.
The monthly sewer service charge is expected to go from about $30 today to $58 in 2020.
City News Service contributed to this story.