If the River Niger bursts its banks, more damage will be caused
Heavy rains have destroyed at least 180 ancient mud buildings in the Unesco-designated world heritage city of Timbuktu.
The floods have also caused the deaths of at least four people in central Mali.
Timbuktu has a poor drainage system meaning that some 30mm of water that fell on the city some two weeks ago had nowhere to go, and soaked into the brittle, hard earth-built walls and foundations.
With more rain now predicted, Mali's authorities said on Monday, that things could get worse if the Niger River spills its banks.
They appealed to residents along Africa's second-longest river to build sandbag barriers on the shores.
People have also been warned to move away from the danger areas.
Timbuktu used to be one of the world's wealthiest cities and was an important Islamic centre.
Some mud buildings, such as Jingereber mosque, date back more than 600 years.
But the isolated city is now one of the poorest in Mali which itself is one of the poorest countries in Africa.
Timbuktu's town hall has been helping to find accommodation for those driven out of their homes, and has paid medical bills for the needy.
The recent rains not only caused the collapse of traditional mud and earth constructed buildings, but also toppled more conventional structures.
Two young children died when water seeped into the walls of their house as they were sleeping.
A man was injured when a two-storey building fell on him, but is recovering.
The government in the capital, Bamako, has set up a crisis committee, to find ways of helping some million Malians, mostly from fishing communities, who live along the river.