When the gates of President Viktor Yanukovych's compound were thrown open on the weekend, Kiev's public gawped in disgusted amazement at the ostentatious luxury in which their leader had lived. Everyone had a favourite symbol of Yanukovych's excess, whether it was the faux galleon on the waterfront, the covered tennis courts or the collection of exotic animals.

But the biggest shock of all to come from the Mezhyhirya compound may yet prove to be not the overblown buildings themselves, but a hoard of documents that the president's henchmen attempted to dispose of as he fled.

Thousands of documents were thrown into the reservoir by the compound, but they were in plastic folders so many floated to the surface. Some of the files were easily skimmed from the top of the water, while others were retrieved from the bottom of the lake by a team of specialist divers, who arrived at Mezhyhirya late on Saturday night to begin their underwater explorations. They also found boxes of live ammunition, apparently tossed away in the last-minute dash to leave the compound.

In one of the many buildings on the estate, Ukrainian investigative journalists are sorting through the stacks of files, in an atmosphere of extreme secrecy. Outside, Igor, a member of the protest movement's car patrol unit, Automaidan, guarded the door, an automatic pistol in his inside jacket pocket. "We have to be very careful who we let in, this is a very sensitive situation," he said.

The decor inside the building is overstated kitsch, deep red and cream carpets complemented by gold-plated wallpaper. But the hub of activity is downstairs, where papers and files cover most of the floor space. Here Ukraine's top investigative journalists have been working in a team, day and night. "People are just grabbing five minutes sleep whenever they can," said Natalia Sedletska of Radio Liberty, one of the group. "There's a sauna room in here, so people hang out in there to warm up."

A team of specialists who have expertise in restoration and archives are giving their services to the team to help them try to preserve as much of the vital information as possible. Some of the files were partially burned before being tossed in the water, showing the panic that accompanied the president's flight.

CCTV footage from the estate released at the weekend shows trucks being loaded with boxes before Yanukovych jumps into a helicopter and flees his palatial compound for good. It seems that the security staff felt they did not have enough time to burn all the documents, and eventually just chucked them in the water. It is clear that a lot of sensitive documents were indeed destroyed, but a first look at what has been retrieved suggests a whole range of scandals could be uncovered.

"These documents are the biggest proof we have of Yanukovych and his regime's corruption," said Sedletska. "There is evidence not only of the dispossessed president's extravagant and luxurious lifestyle here, but also of the culture of bribery, corruption and nepotism."

She alleges there is a large body of documents relating to the massive Mezhyhirya estate and the mysterious firm Tantalit that owned it, and record purchases of the opulent fittings in its mansions, such as a $2m sauna complex, and stone cladding costing hundreds of thousands of dollars. "There are also receipts for millions of dollars in cash payments. Bribes – what else?" Sedletska said. One document supposedly shows billions of dollars flowing into Tantalit in 2007 and 2008.

The documents are being perused by a team of the country's most fearless journalists, who cannot believe their luck at the treasure trove that has been laid out before them.

"We are the ones who have been writing about this place for years, using what ever scraps of information we could glean," said Sedletska. "Now all our investigations are being confirmed. I had to pinch myself when I walked into this place that was once so closely guarded – only days ago I could never have believed this could happen."

Chillingly, among the files recovered from the bed of the river were profiles of some of the investigators themselves, including Tetiana Chornovol, who was badly beaten by thugs on a roadside on the outskirts of Kiev in December 2013.

Members of the controversial women's rights group Femen were among those profiled.

There is no question of the documents being handed over to Ukraine's law enforcement bodies yet, said Sedletska. "We were investigating Yanukovych's corruption and this estate for a number of years, and there was no interest on their part – they are part of the problem," she said. Ukraine's prosecutor general and interior minister, both close associates of the Yanukovych family, were reported to have fled the country.

The documents analysed so far are yielding proof that Mezhyhirya was not only Yanukovych's vulgar version of Versailles, but that it was "the hub of his family's business empire", said Sedletska. "We have found documents here relating to a giant coal trading business in the Donetsk region, that has long believed to be controlled by the Yanukovych family."

The journalists hope that when all the documents have been restored, perused and logged, they will be put online and made available in an open-access archive, called "Yanukovych leaks".

On Sunday, thousands of people again flocked to Mezhyhirya to view Yanukovych's lavish compound with their own eyes, causing traffic jams miles long on the road there. The Ukrainian parliament voted to nationalise the territory, and some MPs have suggested turning into a sanatorium for disabled children.

Of the president himself, nothing has been heard since he appeared in a television interview from an undisclosed location on Saturday night, claiming he was still president. But over the weekend, the leader of his own party said that the president was responsible for "criminal orders", and the Russians also appeared to distance themselves from Yanukovych.

"He has run away, his security and staff have run away … What a pathetic end for a president," wrote Alexey Pushkov, the hawkish head of the Russian parliament's foreign affairs committee, on Twitter.

It seems certain Yanukovych will never live in his luxurious Kiev compound again, but the journalists now going through the documents hope to go one better: to prove beyond any doubt the level of his corruption, and put him on trial.