Judge Carlos Castro Martins barred any work that would interfere with the natural flow of the Xingu river.
He ruled in favour of a fisheries group which argued that the Belo Monte dam would affect local fish stocks and could harm indigenous families who make a living from fishing.
The government says the dam is crucial to meeting growing energy needs.
Judge Martins barred the Norte Energia company behind the project from "building a port, using explosives, installing dikes, building canals and any other infrastructure work that would interfere with the natural flow of the Xingu river, thereby affecting local fish stocks".
Legal battle
He said the building of canals and dikes could have negative repercussions for river communities living off small-scale fishing.
The judge said building work currently underway on accommodation blocks for the project's many workers could continue as it would not interfere with the flow of the river.
The consortium behind the project is expected to appeal against the decision.
In June, the Brazilian environment agency backed the construction, dismissing concerns by environmentalists and indigenous groups who argue that it will harm the world's largest tropical rainforest and displace tens of thousands of people.
The agency, Ibama, said the dam had been subjected to "robust analysis" of its impact on the environment.
The 11,000-megawatt dam would be the third biggest in the world - after the Three Gorges in China and Itaipu, which is jointly run by Brazil and Paraguay.
A judge in Brazil has ordered a halt to construction of a multi-billion-dollar dam project in the Amazon region.