The waste has travelled more than 500km (310 miles) since the dam at an iron mine collapsed two weeks ago.
Samarco, the mine owner, has tried to protect plants and animals by building barriers along the banks of the river.
Workers have dredged the river mouth to help the mud flow out to sea fast.
The contaminated mud, tested by the water management authorities, was found to contain toxic substances like mercury, arsenic, chromium and manganese at levels exceeding human consumption levels.
Samarco has insisted the sludge is harmless.
In an interview with the BBC, Andres Ruchi, director of the Marine Biology school in Santa Cruz in Espirito Santo state, said that mud could have a devastating impact on marine life when it reaches the sea.
He said the area of sea near the mouth of the Rio Doce is a feeding ground and a breeding location for many species of marine life including the threatened leatherback turtle, dolphins and whales.
“The flow of nutrients in the whole food chain in a third of the south-eastern region of Brazil and half of the Southern Atlantic will be compromised for a minimum of a 100 years,” he said.
The magazine Chemistry World quotes Aloysio da Silva Ferrao Filho, a researcher at the respected Oswaldo Cruz Foundation, as saying that the impact has been severe in the river itself.
“The biodiversity of the river is completely lost, several species including endemic ones must be extinct.”
Samarco has erected 9km of temporary floating barriers similar to those used at sea during oil spills in the river to try to hold back the mud from river banks and to protect flora and fauna from the mud.
One concern is that because the mud is high in iron ore and silica it will set hard as concrete when it dries out.
At the mouth of the river, the company has been using heavy equipment to remove sand banks and dredge so that the mud, when it reaches the sea, can flow out as fast as possible and be diluted quickly.
It is the fish and turtle breeding season at this time of year. Local people have been helping get fish into tanks and have been collecting turtle eggs to incubate.
In the meantime, Samarco says it is doing repairs on two other dams it uses to hold waste water which is says are at risk of collapsing.
Eleven people were killed and 12 are missing – presumed dead – in the disaster.
Samarco is owned by mining giants, Vale, from Brazil, and the Anglo-Australian company, BHP Billiton.
It has agreed to pay the Brazilian government 1bn (£170m; $260m) compensation.
The money will be used to cover the initial clean-up and to offer compensation to families.