Vista Gold says a contaminated water treatment program at the Mount Todd gold mine near Katherine appears to be working.

The company says 97 per cent of all toxic metals have been removed from the top 15 metres of water at the open-cut Batman Pit.

The pit contains more than 10 gigalitres of water.

There are also several big waste water holding ponds at the mine site.

Vista Gold wants to get rid of contaminated water at the site so it can move ahead with plans to reopen the mine.

The Northern Territory Mines Department recently issued a waste water discharge licence so the company could release treated waste water into a creek feeding the nearby Edith River.

Vista Gold says the Batman Pit water treatment cost $9 million and used 10,000 tonnes of finely ground limestone.

The Northern Territory Environment Centre says the Government should suspend Vista Gold's water discharge licence until an independent panel can review it.

In the wake of an uncontrolled release of contaminated water from the mine's holding ponds after heavy rains late last month, the Environment Centre's Stuart Blanch says the licence conditions need to be tightened ahead of the next wet season.

"They can have a new waste discharge licence for next wet season, but it should be best practice," he said.

"The company says it wants to prevent any pollution of the Edith River, and it should include all the (pollution) sources on the site, not just the big three (holding ponds).

"That's just common sense, possible, economically sensible and practical."