There’s still oil out there.

The 86-day Deepwater Horizon gusher sent nearly 200 million gallons of oil, tens of millions of gallons of natural gas and 1.8 million gallons of poorly studied chemical dispersants into the northern Gulf of Mexico.

And the fate of much of it remains murky.

“There’s still an awful lot of oil unaccounted for in the environment,” said Ian R. McDonald, an oceanographer at Florida State University who has worked extensively in the gulf.

A massive environmental-crime investigation spearheaded by federal and gulf state officials is underway to tally the harm and has logged tens of thousands of samples from the gulf’s waters, seafloor, marshlands, beaches and wildlife.

At the same time, a handful of independent scientists report that many things aren’t quite right in the gulf. More than 100 square miles of delicate marshland looks sick, they say. The immune systems of certain fishes appear compromised, seaweed and algae production has slowed in places, and a new layer of muck coats the sea bottom near the wellhead. At least a few formerly vibrant deep-sea communities of corals, sea stars and worms now lie dead. Also dead: untold numbers of fish and crustaceans, thousands of birds, and hundreds of sea turtles and dolphins.

While the scientific and legal wrangling over the meaning of this growing mountain of data promises to drag on for years, even ardent environmentalists and cautious government officials agree on one point: The direst predictions of catastrophe sounded during the blowout have not come to pass.

“It’s not as bad as it might have been, but the jury is still out in terms of the full impact of the spill on the health of the gulf,” said Jane Lubchenco, administrator of the National Oceanic and Atmospheric Administration, which is heavily involved in documenting the damage.

Where did the oil go?

Tracking the enormous discharge of oil and gas that surged from the Earth has proved a huge challenge for federal officials who have repeatedly said that nature, in various guises, eliminated much of it.

According to the government’s “oil budget,” released by NOAA in November, a quarter of the oil evaporated or dissolved into the water.

Another 13 percent was blown into fine droplets as it rushed from the broken riser pipe, the report says. Much of this dispersed oil mixed with natural gas from the well and remained deep in the gulf as a thin plume that drifted for months.

The chemical dispersant Corexit 9500 sprayed at the wellhead dispersed another 16 percent into fine droplets, which joined the plume, the report says.

Natural oil-munching bacteria then swarmed the plumes, according to research published in the journal Science in August by Terry Hazen of the Lawrence Berkeley National Laboratory. Three weeks after the well was capped in July, Hazen and his crew no longer found signs of deep oil or gas as they crisscrossed the gulf.

“It disappeared at a much faster rate than anyone anticipated,” Lubchenco said.

In addition to the quarter of the oil that NOAA says nature erased, the Unified Command, led by the U.S. Coast Guard, dispensed with a third of it. Some 17 percent of the total got sucked into the “top hat” lowered onto the broken riser pipe or was otherwise directly recovered, loaded onto tankers and moved to refineries.

Flaring at the surface burned another 5 percent.

Yet prolonged efforts to skim the oil — essentially slurping up slicks on the open ocean — proved largely ineffective, said Stephen Da Ponte, a lawyer in the Coast Guard’s Office of Maritime and International Law. Only 3 percent of the oil was skimmed.

The report was not intended to be an accounting of the final fate of the oil, Lubchenco stressed, but rather a guide to oil recovery.

Still, the budget drew fire from environmentalists and other critics who assailed it as incomplete. Samantha Joye of the University of Georgia said data she collected show that oil at depth, as well as gas, lingered much longer than the oil budget suggests. A scientific publication describing her work is forthcoming.

Much of the criticism focused on the dispersant’s effectiveness, along with whether it damaged, or will damage, wildlife.

And then there’s the “residual” oil — the unaccounted-for stuff. The oil budget puts it at between 11 percent and 30 percent of the total, tens of millions of gallons.

That oil is still out there — on or under beaches, draped across marshes, sunk to the bottom, floating as tarballs.

The scrubbing isn’t over

It’s the job of Coast Guard Cmdr. Dan Lauer to clean it up. He’s the deputy incident commander, directing 2,000 workers and a “couple hundred” boats still scouring the coasts of Louisiana, Alabama, Mississippi and Florida.

His workers find sunken, gooey mats of oil and sand in all four states. They pull tarballs off beaches. They scrape gunk from marshes.

Some 66 miles of shoreline remains moderately or heavily oiled, NOAA reported last month, down from 1,050 at the height of the disaster.

So while the cleanup effort has shrunk dramatically — 48,000 people were enlisted last summer — Lauer anticipates “working hard” through the end of the year, maybe longer.

Crews have paused cleanup efforts on protected islands where birds and turtles nest in the spring, Lauer said. Ultimately, leaving oil mats buried may cause less damage then digging up sensitive habitat, he said.

In the meantime, work crews squeegee oil from the delicate marshes of the Mississippi delta and cut oiled grasses down to the waterline, leaving the roots to grow back. “It’s resilient,” he said.

But new satellite data show that 130 square miles of Louisiana marsh failed to thrive last summer, much more than the usual 24 square miles lost each year. “Instead of greening up, they’re browning up,” said Deepak Mishra, a Mississippi State University geographer who compiled the new data. He suspects the oil, although the satellite images can’t prove it.

Disappearing marsh means two things: A reduced buffer zone for any storms approaching New Orleans, and depleted nurseries and feeding grounds for the shrimp and other species that watermen rely on for their livelihood.

Wildlife’s fate uncertain

More than 1,000 square miles of productive fisheries above the wellhead remain closed, down from 84,000 square miles at the height of the spill.

In a report presented to Kenneth Feinberg, the administrator of the Gulf Coast Claims Facility, John Tunnell Jr. of the Harte Research Institute at Texas A&M University at Corpus Christi wrote that shrimp fisheries would rebound in one to two years, blue crab populations in 2011 should be normal and commercial fish “are not believed to have been significantly impacted.” Oyster beds, which suffered a double hit from the oil and from freshwater flushed into the gulf to push the oil back, will take up to 10 years to recover, the report says.

Ecologists worry that subtle effects of residual oil toxins may further affect the ecosystem, rippling from algae and seaweed all the way up to the sperm whales that dive the northern gulf.

Independent scientists already report disturbing signs. Algae and seaweed looked depleted 70 to 100 miles from the wellhead in December, said Suzanne Fredericq, an ocean biologist at the University of Louisiana at Lafayette. Gulf algae, she said, “are like the grasses on land. If there is something wrong with those algae, you won’t have enough oxygen, and the whole ecosystem, the whole food chain, will be affected.”

At a scientific meeting in February, the University of Georgia’s Joye displayed graphic images of piles of dead, bleached corals, worms, sea stars and other denizens of the deep. The video was collected during submersible dives near the wellhead.

“This is Macondo oil on the bottom, and these are dead organisms because of the oil being deposited on their heads,” Joye said.

NOAA’s Lubchenco agreed that “there is some oil residue on the bottom.” But the “jury is still out on how much of the seafloor is impacted,” she said.

Beyond the fisheries, government agencies and environmental groups are wrangling over the number of birds, turtles and dolphins killed and harmed by the spill.

The bottlenose dolphins have drawn the most attention. In January, an unusual number of dead dolphins began washing ashore across the gulf. About half of the 153 carcasses were very young, perhaps fetal.

Of the 15 most recent dead dolphins, eight “are confirmed to have Deepwater Horizon oil on them,” said Blair Mase, NOAA’s marine-mammal-stranding coordinator for the Southeast.

But NOAA isn’t saying whether that oil killed them, and independent scientists say the agency asked them not to talk about their findings.

Because the cause of death has not been determined, Lubchenco said, “it is premature to speculate until we know more.”

The dolphin data have been vacuumed up in the massive federal environmental-crime investigation, known as a Natural Resources Damage Assessment, which seeks to tally all the ecological harm. BP will then be presented with a restoration bill, which it can dispute. About 90 percent of previous NRDAs have been settled out of court, a NOAA spokesman said.

While NOAA has made some raw data public, it is keeping its conclusions confidential.

“In court proceedings you don’t want to tip your hand too much, because it might jeopardize your case,” Lubchenco said.

That leaves a fairly small group of independent scientists struggling to document damage to the gulf. Just 14 scientific papers have resulted from their efforts, said Lisa Suatoni, a senior scientist for the nonprofit National Resources Defense Council.

Said Christopher Reddy, a senior scientist at the Woods Hole Oceanographic Institution: “We’re only in the beginning stages of putting this puzzle together.”

Staff writers Darryl Fears and Juliet Eilperin contributed to this report.