Look down from a height at any landscape in this slanting autumn light, and you'll see that the ground is only a thin blanket thrown over the remains of the past. The faint marks of fields and walls, houses and roads, show up even in the heart of cities – in relics as humble as the outline of a lost Edwardian rose bed, marring the bland green perfection of a suburban lawn.

The past week has shown once again how hard it is to destroy anything built by man so that it vanishes without a trace. Days after the discovery was announced of a hoard of Anglo-Saxon gold that could have come straight out of Tolkien's Lord of the Rings – but actually came from a dull field in Staffordshire – archaeologists from Southampton University revealed something else that history had completely forgotten.

Half an hour's drive from the modern city of Rome, north of the Tiber and close to Fiumicino airport, a large hexagonal pond in marshy ground marks the vast artificial harbour of Portus, dug from the Mediterranean in the second century to feed the capital of the empire. And here, we now know, there once stood an amphitheatre on the scale of the Pantheon. Archaeologists have been poking around this site for a century, but they either missed or misunderstood the giant heap of rubble, overgrown with weeds. Robbed of its fine marble facing and cut stone blocks, this great building, perhaps used by the emperor himself, was reduced to a ruin almost 2,000 years ago.

More than 140 years ago, the Italian archaeologist Rodolfo Lanciani discovered the building, but seems only to have traced half of it and so interpreted it as a theatre. Professor Simon Keay and his team uncovered the other half, which dramatically changes the understanding of the life of the port. A nearby building is now believed to have been an imperial palace where emperors, including Hadrian, stayed before and after their travels overseas, and possibly received distinguished visitors. The discovery of a superbly carved, colossal marble head – possibly Ulysses – suggests high status, elaborately decorated buildings, not just workaday warehouses and wharves.

Keay compares the importance of the site, and the window it opens on the economic lifeblood of the greatest empire the world had known, to Stonehenge or the great temples of Angkor Wat in Cambodia.

In a world where it sometimes feels as if everything interesting is already known, analysed and available on the internet at the click of a mouse, the ground remains stuffed with secrets. Archaeologists are still working on another great ancient harbour, built when the capital of the Roman empire shifted east to Constantinople. The Emperor Theodosius built his new harbour in the fourth century, and it was found again, complete with shipwrecks still full of their last cargo, when workmen began digging a railway tunnel.

Archaeologists have been feeling their way in for more than 15 years in the murky waters of Alexandria, since divers realised that a new sea wall of huge cement blocks was actually being built on the foundations of a legendary building – the Pharos, the great lighthouse that was one of the seven wonders of the world. Among the treasures they believe may still lie in the sewage-polluted water are Cleopatra's palace, and her tomb.

And in the hectic heart of Mexico city, magnificent carved stones now on display in the British Museum's exhibition on Moctezuma were found when workmen started to dig a new metro station, and hit instead the great temple of the Aztec's island capital Tenochtitlan.

Climate change is exposing many more secrets. As lakes shrivel, coastlines shift and sand blows, lost worlds are uncovered: villages built on stilts in German lakes, flint tools still lying where they were dropped on what is now the bed of the North Sea, whole cities buried in the sands of the Middle East. Often they carry a grim message which modern man might profitably brood over: the sites were lost because the weather worsened, the river changed course, the parched land cracked, the mud brick crumbled, the animals died – and nobody ever lived there again.

• This article was amended on 2 October 2009. The original said that the port was octagonal and that a former amphitheatre on the site had a capacity similar to that of the Colosseum. This has been corrected.