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Twenty years since the Exxon Valdez tanker ran aground in southeastern Alaska on March 24, 1989, spreading an 11-million-gallon crude-oil inkblot into Prince William Sound, the formerly pristine coastal waters once again appear clean and untouched.

Birds like the arctic tern and the endangered Kittlitz's murrelet can be seen skimming the astonishingly beautiful Alaskan coastline while sea otters backstroke through the cold, clear waters of the Sound. It is a remarkable turnaround since the Exxon spill, the worst man-made environmental disaster in U.S. history — the immediate shock of which killed hundreds of thousands of shorebirds that made their home in the Sound along with sea otters that choked on the crude. Over the long term, populations of orcas, killer whales, herring and other species would be injured by the accident. (Read "Remembering the Lessons of the 'Exon Valdez.'")

Today, the coast is clear and clean. But clean is not the same as pristine. Decades ago, some of the spill found its way to a beach on Knight Island in the Sound, a site that scientists studying the accident would designate KN-102 but which during the multiyear cleanup would earn another name: Death Marsh.

Here, on Death Marsh, Mandy Lindberg, a scientist with the National Oceanic and Atmospheric Administration (NOAA) in Alaska's Auke Bay, turns over a shovel of sand and broken rock to reveal a glistening pool of brackish oil. The crude can be chemically typed to the Exxon Valdez, and more oil can be found beneath the beach at Death Marsh and at a number of islands around the Sound. "I wouldn't have possibly believed the oil would last this long," says Lindberg. "Studying the spill has been a great learning experience, but if we had known in the years after the spill what we know now, we would have been looking for oil much earlier."

What scientists like Lindberg know now is that the legacy of the Exxon Valdez is still visible — physically, on the beaches of Prince William Sound and in the animal populations in these sensitive waters that have yet to rebound fully. Using funds from the original spill settlement between Exxon and the state of Alaska, scientists from NOAA have carried out major studies that show oil still remains just beneath the surface in many parts of the Sound — close enough for animals to be affected by it. "The oil may not leak out in quantities that are immediately visible, but that doesn't mean it's not there," says Jeep Rice, a NOAA scientist who has led the studies. "We thought the cleanup would be a one-shot deal — but it's still lingering."

Rice and his colleagues picked a sample of 90 random sites at beaches around the Sound and dug about 100 small pits at each site — more than 9,000 in all. They found oil in over half the places they sampled, despite the fact that only 20% of the beaches that had been hit hardest by the spill, like Death Marsh, were included in the study. Altogether, the NOAA scientists estimated that about 20,000 gallons of oil still remained around the Sound, usually buried between 5 in. and 1 ft. below the surface. (See pictures of the world's most polluted places.)

Those 20,000 gallons, out of at least 11 million spilled, might not seem like much, and scientists initially assumed that whatever oil was left behind during the original cleanup would eventually break down naturally. But it turns out that crude oil — especially when it is spilled in a cold region like southeastern Alaska — lingers in the environment for years. And as long as the oil is there, it can harm the animals that might come into contact with it. Sea otters, for example — the face of the Valdez spill — dig millions of foraging pits in beaches around the Sound, enough to come into contact with oil numerous times. Although the population of sea otters in the area has recovered since the spill, the return has been slow, and researchers suspect the oil might be the reason. "The pattern shows evidence that they're still being exposed," says Rice. "It's not enough to kill them outright anymore, but it's a chronic exposure — and in an environment like this, when species live close to the edge, that could make a difference."

Scientists are still digging into the Sound's beaches, trying to get a better sense of how much oil might be left and whether it will be possible to finish the cleanup. And there are still other questions that need to be answered. The Sound's valuable commercial herring fishery collapsed completely a few years after the spill — there are just 10,000 tons of the fish left today, down from a peak of 150,000 tons before the accident — and researchers are trying to figure out what impact the oil might have had on the species' decline. "We'll never be able to fully link the herring to the oil, but we want to know why the species won't come back and whether it's worth spending the money to help it recover," says Rice.

Exxon-funded scientists have released their own studies, which question the NOAA team's findings and claim that there is little oil left in the Sound. But Rice's studies have held up under peer review — and this reporter personally saw oil buried in a handful of beaches. Ironically, the Exxon spill has greatly enhanced scientists' understanding of the effect that crude oil can have on a vulnerable marine environment: it is more toxic to life than we thought, and harder to clean up. "Even the best cleanup will fall short," says Craig Tillery, a deputy attorney general for the state of Alaska — whose Bristol Bay and Chukchi Sea are being considered for offshore oil and gas exploration — and a member of the Exxon Valdez Oil Spill Trustee Council, which funded the NOAA studies. "You have to make sure this never happens."

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• Bryan Walsh / Prince William Sound
• Two decades after the Exxon Valdez spill, Prince William Sound appears to be thriving again. But scientists are still finding toxic oil hiding underground