There's trouble in the depths. The deep sea is the last true wilderness on Earth, but 1,800 km below the surface, an environmental crisis is growing.

On Monday scientists at the Census of Marine Life (COML) project, the 10-year assessment of the world's oceans completed in 2010, published their analysis of the impact humans are having on the deep sea. Their conclusions were stark: the largest habitat on Earth is being damaged by pollution, resource exploitation and climate change.

The deep sea accounts for 73% of the oceans, an area of 360 million square kilometres. It is a world completely unlike our own. Sunlight cannot reach the depths and the only flickers of light come from living things that use bioluminescence for hunting or disguise.

Far from being a barren wasteland, the deep sea is teeming with life. From vampire squid to blobfish, these extraordinary animals are found nowhere else and their habitats are as unusual as the creatures themselves. Hydrothermal vents, for example, spew out a variety of chemicals on which communities of bacteria can survive without any need for sunlight. There are even forests of coral adapted to live in the cold and dark, providing shelter for more than a thousand animal species.

All of this is under threat. Writing in the journal PLoS One, scientists led by Eva Ramirez-Llodra of the Institute of Marine Science in Barcelona conclude that humans are having severe impacts on the deep sea. In the past it was the dumping of waste that caused the most harm. "Approximately 6.4 million tonnes of litter per year is dropped into the oceans," they write.

Plastics are of particular concern. "There is accumulating evidence that 'mermaids' tears' (5mm in diameter) and microplastics (microscopic sand grain-sized particles of eroded plastic) are becoming more common in the world oceans," says the report. "Little is known however, of the true effect of these particles on the environment and fauna."

The main problems today are fishing and mining. Deep-sea trawling, say the researchers, is particularly damaging because the species caught are "often long lived, with slow growth and delayed maturity making them poorly adapted to sustain heavy fishing pressure."

Hydrothermal vents are beginning to be mined for precious metals such as gold and silver, and rare earth minerals such as cadmium. "Impacts are inevitable, such as habitat and fauna destruction at the mining site," say the scientists.

In the future, climate change will be the biggest problem. Rising carbon dioxide levels will increase the acidity of the oceans, for example, reducing the bioavailability of carbonate ions needed by creatures such as coral and oysters to make their shells and skeletons. "The distribution of cold-water corals already reflects the acidic conditions in the North Pacific but, in the long term, the entire ecosystem could be threatened by acidification," warn the researchers.

Lack of detailed scientific knowledge about the deep sea makes it a difficult environment to protect. One way to stop the damage is to create protected areas. "Management measures such as marine spatial planning and the creation of marine protected areas are very important policy developments that allow us to use resources in the ocean and protect its biodiversity," said Dr David Billett of the National Oceanography Centre in Southampton, who took part in the COML assessment.

A separate study, published on Monday in the Proceedings of the National Academy of Sciences, looked at the distribution of marine mammals around the world's oceans and lakes and concluded their conservation depends on protecting key areas that contain the greatest biodiversity.

Commenting on the deep sea study, Richard Page, a Greenpeace campaigner, said: "At present there is no overarching framework for protecting the marine life of the high seas. Such an agreement would enable the establishment of a network of marine reserves that would safeguard the extraordinary and vulnerable deep sea environments that we are only just beginning to understand."

This uncertainty is also a worry for scientists. Dr Billett said the evironmental impacts on the deep sea environment were moving "much faster than scientists in understanding what is going on ... this is a problem in the deep ocean, this lack of general knowledge."

His colleagues in the COML project agree. "One of the main problems that continue to cause concern is that the fastest movers in the deep sea are those who wish to use it as a service provider," they write. "Lagging behind somewhat are the scientists, managers and legislators."

Camila Ruz is a freelance science journalist who blogs about zoology and popular science books. Follow her on Twitter @CamilaRuzR