The fouled waters of the Animas River are slowly clearing, but the widespread hazards posed by toxic mine waste will be with us for centuries.

Last week, the U.S. Environmental Protection Agency (EPA) accidentally released three million gallons of toxic waste into the Colorado waterway during efforts to clean up a long-defunct gold mine. The spill turned the blue-green waters of the Animas bright orange, and the gunk has spread from Colorado into New Mexico and Utah.

While the colorful incident made global headlines, the situation on the Animas came as no surprise to environmentalists. The EPA estimates that mining has already contaminated streams in the headwaters of more than 40 percent of the watersheds in the American West—and more problems are lurking below Earth's surface. Mining was largely unregulated across much of the West until the 1970s, and today the tunnels of those mines lie abandoned and are often flooded with a toxic stew like the one the EPA accidentally unleashed from Gold King Mine on August 5.

“Abandoned mines sites are sitting out there in the tens of thousands, just in the West, and a significant component of them are releasing this acid mine drainage to receiving waters,” says Ronald Cohen, a professor at the Colorado School of Mines and at North-West University in South Africa.

So what is it about mining that generates so much toxic material? The nasty-looking runoff that inundated the Animas River was created from a set of seemingly benign ingredients. The process begins when groundwater, rainwater and snowmelt, kept in check by pumps while the mine operates, fill up the tunnels once the site is abandoned. The water mixes with pyrite (iron sulfide) and the mine's air to produce hydrogen ions and sulfates—which pair up to form sulfuric acid. As if that acid isn't bad enough, it soon goes to work dissolving metals like iron, aluminum and manganese, as well as metalloids like arsenic, from the rocks commonly found in and around mines.

“Toxic metals are most soluble when the acidity is high, when the pH levels are low,” Cohen explains. “So when the pH goes down to pH 3, pH 2, the metals are very soluble and the acid sort of feeds back to dissolve those metals and make the water even more toxic.” Once a volume of watery toxic waste forms, the job of handling it safely becomes very difficult. The first step, Cohen notes, is to try to keep waste inside the mine until it can be removed and treated at a controlled rate. “You put a cork in it,” he says.

If the EPA has enough funding to tackle a site with best practices, they might install a 12-foot-thick reinforced concrete bulkhead to keep water inside the mine. Bulkheads are fitted with pipes so that when water builds up in the mine, it can be released through the pipes at a controlled rate for treatment. The Gold King Mine was blocked with a dam of bulldozed rock, Cohen adds, which is a less expensive but common method of containment. The EPA accidentally breached that plug while attempting to fit a pipe for water treatment, according to statements from the agency's on-scene coordinator Hayes Griswold.

Some catastrophic runoffs like the Animas spill produce a shocking visual effect, staining the water with hues so distinctive they've been made into their own paint colors. But many of the abandoned mines in the U.S. and around the world create less dramatic but equally disturbing pollution that makes far fewer headlines.

“Water has this habit of finding the path of least resistance," Cohen says. "So it goes from coming out one place to coming out in every little fracture around the mountainside.”

Even when mine waste can be safely contained, cleaning it up requires money and commitment over the span of many lifetimes. “You're going to be treating, as they say, in perpetuity,” Cohen explains. “Now, I've done work in South Africa where we've calculated when the oxygen may run out inside a particular mine and found out it's not really perpetuity but 200 years. But a mindset of treating for perpetuity is the way you have to approach it.”

Treatment might mean anything up to and including a multistage water treatment plant, but that's something rarely seen in the world of mine remediation. Far more common is construction of a watery pit that employs the flip side of the chemical equation that loaded the water with metals in the first place.

“Just as acidic water dissolves the metals, if you make the water in a pit very basic in nature—a pH significantly above 7—then you knock those dissolved metals out of the solution and they settle to the bottom of the pit,” says Cohen. Four such ponds have been built to capture and treat water at the Gold King Mine site, EPA Administrator Gina McCarthy said on August 11 during a previously scheduled appearance at the Washington research group Resources for the Future. Ponds of this type, however, must be safely maintained. That can be a difficult proposition, as evidenced by the failures of many such structures around the world—including a water treatment tailings pond that unloaded on the Animas River watershed in 1974.

Luckily, it's looking like the short-term human health impacts from the recent downstream surge will be minimal. Even though extremely high levels of contamination have been reported in some places, humans can limit their exposure by avoiding swimming or fishing in the river and not drinking its water. Wildlife, of course, has no such option. Acidity levels control aquatic organisms' ability to keep contaminants from crossing membranes in their bodies. Fish, for example, may admit toxic metals across their gills when pH plunges, and they become less efficient at transferring oxygen across their gills to breathe.

So far, most reports from the Animas River suggest relatively good news for fish and perhaps for other aquatic species subjected to the initial spill. The spill moved downstream so quickly it wasn't likely to have caused significant health effects to animals in the river system, EPA toxicologist Deborah McKean said Tuesday, according to the Associated Press. Work by Colorado Parks and Wildlife has also been encouraging. Before the yellow plume reached Durango, biologists intentionally put 108 caged fingerling trout into the waters there. With the exception of one fish, which died immediately of apparently unrelated causes, all of them survived six days of swimming in the fouled water, which was a surprise to agency spokesman Joe Lewandowski. “That plume of acid runoff looked pretty bad. Survival, honestly, wasn’t expected,” he told the Durango Herald.

Johnnie Moore, a University of Montana geologist, was also encouraged by the lack of obvious mortality: “Generally when there are events like this, if they are very toxic and the pH drops very low, you'll see dead fish all over the place,” Moore says. “In the old days in the Clark Fork River here in Montana, when we had releases of mining contaminants on floodplains during storms, you'd see hundreds and thousands of fish floating belly-up in the river. I've seen no reports of dead fish like that, so that's a good thing.”

But the immediate impacts of a spill are only part of the problem, Moore cautions. “Aquatic ecosystems tend to be pretty resilient if you don't have a residual of contaminants that have an effect. So that's really the issue for the longer term. How much contaminated sediment ended up in the boulders and rocks down in the bed and in the shallows alongside the river? And how long will that stuff stay there kind of oozing out metal and having longer-term effects? Those are much more subtle, but they are quite real.”

During studies on the Clark Fork River, Moore and his colleagues noted that stretches with high metal contamination produced fewer and less diverse insects. In turn, the fish that ate them didn't grow as well and suffered more diseases. And once the river is reopened for human use, there are risks that people will eat fish that have accumulated toxins like mercury or lead at harmful levels.

Unfortunately, there are no good options for remediating the damage downriver once a spill occurs. Trying to dig and remove contaminated sediments would be more harmful to the ecosystem than simply leaving it alone, Moore says. “Instead we're looking at natural remediation—which means that you have to let it be contaminated, you have to monitor it, you have to manage it so people aren't being affected, because there's not a heck of a lot you can do with wildlife, and you've got to hope for the best.”

For the Animas, the best case would be lots of snow this winter. A big snowpack and a long high-runoff season would be an ideal aid to nature's own remediation efforts, Moore says. “That moves sediment from tributaries that are not contaminated, which mix with and dilute the contaminated sediments, so by the time you get to Lake Powell you've not only dumped the contaminates in the lake's delta, but also mixed them with a bunch of fine grain sediments to bury them there.”

As for the rest of the nation's abandoned mines, it's still unclear how the Animas spill will influence efforts to mitigate their risk. The known numbers of abandoned mines across the West and the world are daunting enough, Cohen adds, but to make matters worse, the surveys of such sites typically include the caveat that much more work is needed on the ground to determine just how many mines are really out there.

“It's a very big problem—it's a combination of problems really,” he notes. “The hazard of these abandoned mines is a focus of EPA and the states, but because they are abandoned there's generally no identifiable, responsible party who caused this problem that you can access anymore. So these places are just sitting out there in very large numbers.”