The waterhole complete with a preserved wickerwork lining was revealed during excavations in Heslington village.
The structure also contains fragments of wood giving clues to the landscape of the time, about 2,500 years ago.
The university's archaeology department plans more digs at the site, which also contains an important Roman building.
The university plans to open the site to local archaeological community groups as well as allowing students access to a live dig.
'Fantastic opportunity'
Steve Roskams, of the Department of Archaeology, said: "Exciting archaeological discoveries very often follow hot on the heels of planned commercial developments. That's what has happened here.
"It's a fantastic opportunity to learn more about what our local landscape was like thousands of years ago, and we intend to make the most of it."
Initial analysis suggests that the only evidence of high-status Roman architecture dates from quite late in the Roman period.
"If this is confirmed," said Mr Roskams, "it could indicate that York was essentially little more than a military enclave during the early part of the Roman occupation, only developing into the full-scale imperial settlement of Eboracum centuries later."
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