It has been the biggest and most comprehensive attempt ever to answer that age-old question – how many fish are there in the sea?

Published today, a 10-year study of the diversity, distribution and abundance of life in the world's oceans attempts just that. The Census of Marine Life, which hopes to paint a baseline of marine life, estimates there are more than 230,000 species in our oceans.

"From coast to the open ocean, from the shallows to the deep, from little things like microbes to large things such as fish and whales," said Patricia Miloslavich of Universidad Simón Bolívar, Venezuela and co-senior scientist of the COML. The study also covers crabs, plankton, birds, sponges, worms, squids, sharks and slugs.

A team of more than 360 scientists around the world have spent the past decade surveying 25 regions, from the Antarctic through the temperate and tropical seas to the Arctic to count the different types of plants and animals.

The results show that around a fifth of the world's marine species are crustaceans such as crabs, lobsters, krill and barnacles. Add in molluscs (squid and octopus) and fish (including sharks) and that accounts for up to half of the number of species in the world's seas. The charismatic species often used in conservation campaigning – whales, sea lions, turtles and sea birds – account for less than 2% of the species in the world's oceans.

The surveys have also highlighted major areas of concern for conservationists. "In every region, they've got the same story of a major collapse of what were usually very abundant fish stocks or crabs or crustaceans that are now only 5-10% of what they used to be," said Mark Costello of the Leigh Marine Laboratory, University of Auckland in New Zealand. "These are largely due to over-harvesting and poor management of those fisheries. That's probably the biggest and most consistent threat to marine biodiversity around the world."

The main threats to date include overfishing, degraded habitats, pollution and the arrival of invasive species. But more problems are around the corner: rising water temperatures and acidification thanks to climate change and the growth in areas of the ocean that are low in oxygen and, therefore, unable to support life.

The COML identified enclosed seas such as the Mediterranean, Gulf of Mexico, China's shelves, Baltic, and the Caribbean as having the most threatened biodiversity. "Enclosed seas have the risk that, when you impact it and throw chemicals or other garbage into it, it will not go away so easily as it will from the open ocean," said Miloslavich.

Dense coastal populations of humans also tend to be packed along enclosed seas, meaning increased pollution and extraction of more biodiversity from the water.

The Mediterranean, which contains almost 17,000 identified species, scored the maximum threat rating of five for four of the categories. Scientists studying the Mediterranean identified problems related to increased litter from shipping and munitions across the sea as well as bombs discharged during the Kosovo war.

The Mediterranean also faces problems because of invasive species displacing the creatures that already live there. This sea had the most alien species out of all the 25 regions surveyed by the COML, with more than 600 (4% of the all species present). Most had arrived from the Red Sea via the Suez Canal.

The most diverse regions identified by the COML are around Australia and south-east Asia. "It's also a hotspot for terrestrial biodiversity as well and this has been known for about 100 years," said Costello.

"It looks like that region with the coral reefs has always had a very high rate of speciation. It also has a very diverse range of habitats – from the deepest areas of the oceans to large areas of shallow seas, which can support coral reefs."

Both Australian and Japanese waters contain more than 30,000 species each and are among the most biologically diverse in the world. Next in line are the oceans off China, the Mediterranean Sea and the Gulf of Mexico.

Apart from algae and the seabirds and mammals that travel around the sea, the COML identified the manylight viperfish (Chauliodus sloani) as the most "cosmopolitan" marine creature. Its presence was recorded in around a quarter of the world's seas.

"This inventory was urgently needed for two reasons," said Costello. "First, dwindling expertise in taxonomy impairs society's ability to discover and describe new species. And secondly, marine species have suffered major declines – in some cases 90% losses – because of human activities and may be heading for extinction, as happened to many species on land."

Miloslavich said the COML data would "allow policy-makers to make better and more informed decisions on what areas should be protected for the better management of resources and the ecosystems as well, in order that they keep providing good services."

The results of the survey are published today online at the PLoS ONE journal. More detailed results will be published in October, at which time the COML will confirm how many species it estimates are in the world's oceans.

And for every marine species of all kinds known to science, COML scientists estimate that at least four have yet to be discovered. They said that around 70% of species of fish have been discovered, for example, but for most other groups likely less than one-third are known. As of February, the number of marine fish species known to science stood at 16,764, and was growing at around 100 a year.

Scientists estimate that there are almost 22,000 fish species in the world.

The most fruitful potential areas for discovery include the tropics, deep seas and southern hemisphere.

"At the end of the Census of Marine Life, most ocean organisms still remain nameless and their numbers unknown," said Nancy Knowlton, a biologist at the Smithsonian Institution, leader of the COML's coral reef project. "This is not an admission of failure. The ocean is simply so vast that, after 10 years of hard work, we still have only snapshots, though sometimes detailed, of what the sea contains. But it is an important and impressive start."