Hundreds of beached dolphin carcasses, shrimp with no eyes, contaminated fish, ancient corals caked in oil and some seriously unwell people are among the legacies that scientists are still uncovering in the wake of BP's Deepwater Horizon spill.

This week it will be three years since the first of 4.9 million barrels of crude oil gushed into the Gulf of Mexico, in what is now considered the largest marine oil spill in the history of the petroleum industry. As the scale of the ecological disaster unfolds, BP is appearing daily in a New Orleans federal court to battle over the extent of compensation it owes to the region.

Infant dolphins were found dead at six times average rates in January and February of 2013. More than 650 dolphins have been found beached in the oil spill area since the disaster began, which is more than four times the historical average. Sea turtles were also affected, with more than 1,700 found stranded between May 2010 and November 2012 – the last date for which information is available. On average, the number stranded annually in the region is 240.

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Contact with oil may also have reduced the number of juvenile bluefin tuna produced in 2010 by 20 per cent, with a potential reduction in future populations of about 4 per cent. Contamination of smaller fish also means that toxic chemicals could make their way up the food chain after scientists found the spill had affected the cellular function of killifish, a common bait fish at the base of the food chain.

Deep sea coral, some of which is thousands of years old, has been found coated in oil after the dispersed droplets settled on the sea's bottom. A recent laboratory study found that the mixture of oil and dispersant affected the ability of some coral species to build new parts of a reef.

Doug Inkley, a senior scientist for the US National Wildlife Federation and author of a report published this week on wildlife affected by the spill, said: "These ongoing deaths – particularly in an apex predator such as the dolphin – are a strong indication that there is something amiss with the Gulf ecosystem."

Scientists believe that the 1.8 million gallons of dispersant, sprayed as part of the clean-up, have cemented the disaster's toxic effect on ocean life and human health. The dispersant, called Corexit, caused what some scientists have described as "a giant black snowstorm" of tiny oil globules, which has been carried around the ocean in plumes and has now settled on the sea floor. A study last November found the dispersant to be 52 times more toxic than the oil itself.

Larry McKinney, director of the Harte Research Institute for Gulf of Mexico Studies, said: "Before we depend on dispersants to get rid of oil and get it out of sight, we need to understand what it can do in the open ocean. We're told to keep oil off the shore and away from estuaries, but we've not dealt with something like this before, that's in the open ocean and gone from top to bottom, affecting the whole water column."

Scientists believe the addition of dispersants to the oil made it more easily absorbed through the gills of fish and into the bloodstream. Dr William Sawyer, a toxicologist, has studied concentrations of petroleum hydrocarbon (PHC) in edible fish and shellfish in the region. Samples before the spill had no measurable PHC in the tissue, whereas fish tested in recent months show tissue concentrations as high as 10,000 parts per million, or 1 per cent of all tissue. He said: "The study shows that the absorption [of the oil] was enhanced by the Corexit."

BP says the dispersants it used are "government approved and safe when used appropriately", and that extensive testing has shown seafood in the Gulf states is safe to eat.

Louisiana State University's Department of Oceanography and Coastal Sciences has found sea life in the Gulf with lesions and deformities that it believes may be linked to the use of dispersants. These include shrimp with no eyes and crabs with no eyes or without claws. BP claims these abnormalities are "common in marine life", had been seen in the region before, and are caused by bacterial infections or parasites.

In a blow to the region's tourism, tar balls continue to wash up along the affected coastline, which now stretches from the beaches of Louisiana to Mississippi, Alabama and Florida. Marco Kaltofen, a chemical engineer at the Worcester Polytechnic Institute, said: "We have a reservoir of petroleum and petroleum-contaminated sediment that lies just offshore of several Gulf beaches. Every time we have a storm, all of a sudden you're getting these tar balls washing up."

It is not just wildlife that scientists believe has been affected. Michael Robichaux, a Louisiana doctor, has documented 113 patients who he thinks were made ill by exposure to chemicals associated with the spill. Their most common symptoms include headaches, memory loss, fatigue, irritability, vertigo, nausea, blurred vision and insomnia.

One of Dr Robichaux's patients, Jorey Danos, 32, is a formerly healthy father of three. Since working for BP on the clean-up, he says he has experienced serious ill health, including severe abdominal and joint pain that has left him walking with a cane. Several doctors, including a neurologist, have put his condition down to the neurological impact of exposure to the chemicals related to the spill.

Mr Danos said: "I worked 21 days in one of the boats skimming the oil and we were sprayed directly with Corexit from above on three occasions. My skin came out with bumps and burning and I started having breathing problems. When a speedboat with BP representatives came by I asked for a respirator but they said no, because it would lead to bad media attention. Now I'm still dealing with it three years later." BP said all workers were provided with safety training and protective equipment and would have had the opportunity to join a class action settlement.

Geoff Morrell, BP's head of US communications, said: "No company has done more to respond to an industrial accident than BP has in the US Gulf of Mexico."