The city admits the system can overflow wastewater in several areas of the city and has for years.
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At one point, the feds wanted the city to spend $7 billion to fix it.
Mayor Sylvester Turner says he and his team negotiated it down to a little more than $2 billion.
That money will come from people who pay Houston water bills.
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"Yes, there's a cost associated with it, but we now have the responsibility of making sure that as people pay more over the next 15 years, that we are solving the problem," Turner said.
If the $2 billion cost is spread among all Houston water bills, it would mean a $23 a month increase added to every bill, every month for 15 years.
That is just an average. The city hasn't decided how to spread the cost.