The site, close to the Algerian capital's UNESCO-listed casbah, has yielded remains from the city's Roman, Byzantine, Ottoman and French periods.
"It was spectacular," said archaeologist Kamel Stiti, co-director of the excavations. "In one look, you could see two millennia of Algiers' history."
The remains, on the location of a Roman port town called Icosium, were discovered in 2009 when the ministry of culture ordered surveys along the planned metro line.
They also found parts of the Ottoman-era Es Sayida mosque, which French authorities flattened in 1831, shortly after their conquest of the North African country.
The colonial government put a public square in its place and called it King's Square and later, Government Square. It was re-named Martyrs Square after the country's hard-won independence in 1962.
Experts had believed that few pre-colonial artefacts remained on the site, but many of the ruins turned out to be surprisingly well-preserved, Stiti said.
The site will now become a museum incorporated into the station, which, in turn, will take up less than half its planned 8,000 square metres.
The tunnel will go as deep as 35 metres (115 feet) in order to work around the remains.
The Martyrs Square station is set to open in November, part of an extension to the main metro line inaugurated in October 2011.
The museum will open shortly afterwards, covering 1,200 square metres and organised chronologically.
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