The demonstration of activists and migrants was to protest at the eviction of 455 migrants, most of them from Sudan and Eritrea, from the city's Square Daviais, where they had set up camp.
A small group moved into the square in June but their numbers grew when two squares in privately owned building were cleared and with the arrival of more migrants from Italy and Spain.
There was only one tap providing water and one toilet in the camp and the presence of rats was reported, along with cases of scabies.
The square was cleared, on the order of the representative of central government in the region, on 23 July, with the city council claiming that 147 of the "most vulnerable" occupants had been offered shelter.
On Thursday a former lycée, in which 261 had been lodged with the help of NGOs, was evacuated because, the council said, it is being converted for use as a school.
A small number of tents have since reappeared on the Square Daviais.
Nantes and the surrounding area have seen a "significant rise" in the number of migrants arriving since February and an increase of 28 percent over the past year, officials say, while the number has fallen in most French cities.
On Friday the city of Lille held a ceremony to celebrate the granting of asylum to 62 Sudanese refugees who had been rescued by the Aquarius humanitarian boat in the Mediterranean.