Teasing out what might have been caused by the spill and what is normal will be tricky, and that's the challenge scientists now face. Deformities, diseases and sudden shifts in fish numbers are regular occurrences in nature. For example, scientists are not sure what to make of reports from fishermen of eyeless or otherwise deformed shrimp and crabs.
"I've heard everything but shrimp with two heads," said Jerald Horst, a marine biologist retired from LSU AgCenter who writes books about the Gulf. "I listen respectfully. Reports can be useful but are not proof in themselves of cause and effect."
Even if oil were pinpointed as the cause, it could be difficult to definitively tie the problem to the BP spill. The Gulf is strewn with wells, pipelines, natural oil leaks from the seafloor, and pollution from passing ships. And muddy, contaminant-laden water flows constantly into the Gulf from the Mississippi River.
Still, the more scientists look — thanks to millions of dollars in research money, much of it coming from a fund set up by BP for independent research — the more they're finding that may be off-kilter.
For example, last year scientists with the University of Louisiana at Lafayette took cruises in search of crabs, lobsters and seaweed they had been studying in the waters not far from the BP well. They found a surprising lack of diversity.
There saw less seaweed and fewer crabs, lobsters and other forms of life. Also, crustaceans they pulled up had lesions, lost appendages and black gunk on their gills, said Darryl Felder, a biologist at ULL. He said the black coating may be associated with the large amounts of drilling mud used to try to plug the leaking well.
In Barataria Bay, which was hit hard by the spill, scientists say they found dolphins that were anemic and showing signs of liver and lung disease. Those problems have not been linked to the spill. But in the same bay, scientists say they have linked oil contamination to genetic changes in bait fish known as killifish.
Near the BP well, scientists have found a dying community of deep-sea coral. The scientists recently published findings linking its demise to oil that was chemically fingerprinted as having come from the BP well.
Last year, the National Oceanic and Atmospheric Administration advised fishermen to throw suspicious-looking fish back, and fishermen say they have been doing that. At the same time, the Food and Drug Administration and state agencies say they have tested Gulf seafood extensively and found no problems, and researchers agree there is little cause for concern.
"It's not a people issue, and people should not be concerned about fish entering the market," Murawski said.
For the second year, fishermen like Wayne Werner, who catches red snapper commercially, are calling in with reports of lesions. He and others said they want to get to the bottom of the problem, which is forcing them to take longer trips to fishing spots outside the spill zone and making them fear for their livelihoods.
"Every time we talked about bad fish, everybody kind of went nuts on us. Just like, 'You're hearsaying,' you know? And we're saying, 'Well, they're there,'" the Louisiana boat captain said this week. "They're still there. Now that the water is getting warm again, we're starting to see more and more again."