The flooding caused mud and rubble to pile in Cyrene's Greek-era baths that will require specialised clearing said local antiquities department official Adel Boufjra.
He warned that although the damage so far has been slight, the flooding may have added to subsidence that could later topple one of the monuments.
"I'm pretty sure, and expecting, that one of these landmarks could collapse due to the excessive underground water during the winter," he said.
While that risks great damage to the picturesque ruins at Cyrene, known locally as Shehat and a draw for travellers since the 18th century, the water has also washed clear a previously unknown Roman drainage system, Boufjra said.
"The flooding has revealed a new site - a water canal that I believe dates back to the Roman era. It is a distinctive discovery for the city," he said.
Scientists at the World Weather Attribution, an international research group, said climate change had caused up to 50% more rain during the storm than would previously have been the case - underscoring future risks to heritage.
Cyrene was a Greek colony and one of the principle cities of the ancient Hellenic world before becoming a major centre under the Romans until an earthquake destroyed it in the year 365.
One of Libya's five UNESCO World Heritage sites, along with the extensive Roman ruins overlooking the Mediterranean at Sabratha and Leptis Magna, Cyrene's stone pillared temples stand on a fertile hillside near rocky crags.
