The authorities in the state of Rio Grande do Sul state that the dead animals have been affected by bird flu.
Brazil issued an animal emergency in May after several cases of bird flu were detected.
The new deaths come after nearly 400 dead seals and sea lions washed up on beaches in Uruguay in September.
Earlier this year, 55,000 wild birds and 585 sea lions died of bird flu in Peru. This summer, the World Health Organization (WHO) warned that bird viruses that spread to mammals pose an increased threat to humans.
Chile and Argentina have also reported cases of bird flu in aquatic animals.
Brazil remains classified as free from the disease, as no cases have been detected in commercial chicken farmers.