Officials were shocked when they discovered how toxic the closed Prohibition and Alexander mines near Reefton were last year, Environment Minister Nick Smith says.
In 2013, the Government estimated the cost of cleaning up the mines would be $600,000.
But yesterday, it announced it would cost $3 million to clean up what it calls the country's most contaminated site.
The mines have some of the highest levels of arsenic in the world, while the water is 33,000 times over the safe limit for drinking, although it is not out in the open.
Dr Smith says Envirowaste has been hired to do the work, which will start in two weeks and finish by the end of the year.