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The day it happened, biologist Jim Bodkin was watching sea otters off the coast of Big Sur, Calif. In Seward, Alaska, orca researcher Craig Matkin tinkered beneath the bow of his 42-foot purse seiner, Lucky Star. One hundred forty nautical miles to the east, Capt. Dave Janka stood in the kitchen of his family’s remote cabin, hand-grinding coffee and listening to public radio on a Walkman. When the news came on, he nearly “dropped the whole thing.” Then he jumped in his Zodiac and motored eight miles to one of the greatest environmental disasters of our time: the Exxon Valdez tanker foundering on a reef, hemorrhaging 11 million gallons of crude into Prince William Sound. It was March 24, 1989.

The early-morning scene was eerily calm, but word was spreading. As Janka idled his skiff, Matkin and thousands of other Alaskans hastily jammed gear into boats, cars and planes and swarmed toward the Sound, which had nowhere near enough equipment on hand to tackle the spill.

Worse, while Exxon mustered its resources, a winter storm blew in, driving crude against shore and into the Gulf of Alaska. Oil coated more than 1,000 miles of beaches, none with road access. Hundreds of thousands of sea birds and mammals washed up dead. Even after a cutting-edge “supersucker” was barged in from Prudhoe Bay, volunteers armed with bath towels and five-gallon buckets handled the bulk of the cleanup. “I was out for I don’t know how many days straight,” Matkin says. “The feeling of weightlessness was like being in outer space.”

If the devastation had a silver lining, it was the billion-dollar settlement paid to the Exxon Valdez Oil Spill Trustee Council in 1991. The money bankrolls an ecosystem-monitoring program called Gulf Watch Alaska that includes Matkin, Bodkin and 21 other scientists. With 25 years of data and enough funding for 18 more, Gulf Watch is providing the first comprehensive, long-term look at a marine oil spill’s consequences – knowledge that could guide response to other spills and, as oil exploration and shipping heats up in the Arctic, even help prevent them.

Scientists predicted Prince William Sound would recover within 15 years, but today, residual oil continues to harm both human and ecological communities. “It’s very insidious,” says Mark Carls, a toxicologist with the National Oceanic and Atmospheric Administration. “I think we were all surprised.”

Thirteen of the 35 whales in the Sound’s resident, fish-eating pod died soon after the spill and the group still hasn’t recovered.

“You think about oil spills and you think of those photos of oiled otters and birds dying on beaches,” adds Dan Esler, a wildlife biologist with the U.S. Geological Survey. “But chronic effects for some species can be of the same magnitude as the immediate effects.”

Today, it’s hard to imagine a Prince William Sound battered by environmental catastrophe. Green-shouldered mountains plummet to the sea. Kayakers paddle beneath glaciers. Bald eagles keep watch over rugged, rocky beaches.

If you know where to look, though, there’s no shortage of oil. Officially, 21,000 gallons remain, but many consider the estimate conservative. And because much of it is trapped beneath rocks and cut off from oxygen, it has the same composition as oil that’s only 11 days old. Even where oil is exposed to the elements, Carls says, the hydrocarbon molecules that persist longest also tend to be the most toxic. That might explain why some species – like Craig Matkin’s orcas – are still reeling.

Matkin’s fascination with orcas began in 1976, when he first encountered them as a young salmon biologist. By the time of the spill, he could recognize individual whales on sight. They were like family – which made seeing them slicked in oil all the more painful.

Thirteen of the 35 whales in the Sound’s resident, fish-eating pod died soon after the spill and the group still hasn’t recovered, even as other Alaskan orcas are thriving. Worse off are the genetically distinct “Chugach transients,” which pass through Prince William Sound as they roam the coast hunting seals and sea lions. The pod had 22 members before the spill; today, there are only seven. Because they’re at the top of the food chain, the Chugach transients accumulate contaminants from everything below them. High levels of PCBs and DDT in their blubber may be causing reproductive problems: The Chugach transients haven’t birthed a single surviving calf since 1984.

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Other creatures, like sea otters and intricately patterned harlequin ducks, are only now approaching recovery. Otter and duck biologists had braced themselves for large death tolls, because animals that rely on fur or feathers for warmth are susceptible to hypothermia after oil exposure. They can also suffer immune suppression and organ dysfunction from ingesting oil via grooming. But when populations failed to rebound after 12 years, Esler and Bodkin were baffled. They began scrutinizing the animals’ underwater routines, eventually learning that the invertebrates they eat in the intertidal zone, like clams and mussels, were full of oil. Invertebrates don’t metabolize oil as well as vertebrates, so otters and harlequins were ingesting it long after the spill had been cleaned up.

Though the mechanism of injury for some species has become clear, the collapse of Prince William Sound’s herring fishery remains a mystery. Today, many researchers say herring – tiny silver fish eaten by nearly everything – are the species most impacted by Exxon Valdez. Unfortunately, the fishery collapsed during a lull in funding “when no one was looking,” laments Scott Pegau, coordinator of the Herring Research and Monitoring program, run by the Prince William Sound Science Center with funding from the Oil Spill Trustee Council. Industry-funded scientists therefore argue that it can’t be linked directly to the spill.

Pegau suspects that oil exposure suppressed herring’s immune systems, leading to a disease outbreak, or that a dearth of zooplankton after the spill left the fish malnourished. Whatever the cause, the economic impact still stings in fishing villages like Cordova, where herring’s boom-and-bust population cycles have historically mirrored those of Sitka, Alaska. Yet for the past 20 years, Cordova fishermen have been sitting on their hands while the Sitka fishery remains productive. “Herring used to be what woke Cordova up from its winter slumber,” Pegau says. “Now we don’t get going until May.”

This year, though, there’s cause for hope: Pegau counted 2,100 schools of juvenile herring in 2013, compared to 150 three years ago. Fishermen who’ve held herring permits for generations stop him on the street to ask when they can fish. His answer is cautious: “We won’t know for sure for a couple more years.”

Exxon Valdez also left some positive legacies. The Oil Pollution Act of 1990 requires single-hull tankers to be fully phased out by 2015, a goal that’s nearly achieved, says Betty Schorr of the Alaska Department of Environmental Conservation. And regulations “aren’t hypothetical anymore,” she adds: Alaska’s standard response plan now spans three days (the window of good weather after Exxon Valdez) and crude tankers must be capable of dealing with an Exxon-sized spill to operate in state waters.

But Alaskan jurisdiction extends just three miles offshore. After that, responsibility falls to the Coast Guard, which allows ships in western Alaska to circumvent certain regulations because the emergency response infrastructure needed to comply with them simply doesn’t exist there. That’s exactly why environmental watchdogs think extra precaution is warranted: As the ice-free season grows longer, more international tankers are passing through Arctic and Aleutian waters without stopping at Alaskan ports, where they’d be subject to state laws. Plus, given the remoteness and extreme weather, a slip-up – either from a shipping vessel or the drilling proposed by Shell – could be disastrous. “The Arctic is a grave concern of ours,” Schorr says.

Prince William Sound communities may be the nation’s best prepared to deal with environmental disaster, with extra precautions like satellite monitoring of fully laden tankers and “escort ships” to flank them, as well as programs like Gulf Watch that provide a solid understanding of the marine environment. Yet many of the lessons learned there aren’t being applied elsewhere. “Deepwater Horizon was a great example,” Bodkin says, referring to the 2010 Gulf of Mexico disaster. “A lot of us that worked on Exxon Valdez were frustrated because we felt the mistakes we made were simply repeated 20 years later.”

The most significant, Bodkin says, was the lack of baseline data. “That was our primary recommendation: Where oil and gas is developed, extracted or transported, we need to have a good understanding of the ecosystem prior to a spill.” Monitoring was almost as inadequate in the Gulf of Mexico in 2010 as it was in Prince William Sound in the ’80s, Bodkin adds, making it harder to assess damage. “The yardstick we have to measure recovery is really hampered by a lack of knowledge of what the system was before.”

In Alaska, at least, the message has partly sunk in: Oil exploration in the Chukchi and Bering seas has prompted more robust research. “We know far more about how (those places) operate, from both the physical and biological side, than we knew about Prince William Sound,” says Tom Weingartner, an oceanographer at the University of Alaska Fairbanks who works in both locations.

That’s reassuring for Dave Janka, who’s constantly reminded of the Exxon Valdez as he drives researchers to field sites in his charter boat. Every year, Janka revisits some of Prince William Sound’s remote beaches to turn over rocks and photograph residual oil. And every year, he finds not only the gooey substrate left over from Exxon Valdez, but also tiny, hardened globs of oil from the 9.2-magnitude earthquake that ruptured onshore oil storage tanks and killed 115 Alaskans in 1964.

This month, on the 25th anniversary of the spill and the 50th anniversary of the earthquake, Janka will be prepared: “I’m going to go camp out on top of a mountain,” he jokes, “and wear my lifejacket and hardhat to bed.”

Krista Langlois is an editorial fellow at High Country News.

This article appeared in the print edition of the magazine with the headline The toxic legacy of Exxon Valdez.

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