"Who can live on 100,000 pesos?" protest leader Zoila Bustamante said Wednesday. "What a joke!"
Although southern Chile sees red tides every year, this year's extended further north than usual, Jorge Navarro of the marine institute IDEAL said.
"It affected bivalve populations (such as clams) that had never before been exposed like this" to the algae, he said.
On the shores of Santa Maria Island off the center of Chile's long coast, cuttlefish have washed up dead in the thousands.
Various beaches in the center of the country were closed, meanwhile, as specimens of the dreaded Portuguese Man-of-War jellyfish, normally foreign to the area, floated nearby.
Shifting oceans Scientists largely blame the anomalies on El Nino, a disruptive weather phenomenon that warms sea surface temperatures in the equatorial Pacific.
With its 2,485 miles of Pacific coastline, Chile is particularly exposed to the effects of El Nino, which strikes every few years.
"We think that a common factor in the deaths of creatures in southern Chile, in the salmon farms and in fish off the coast is the El Nino phenomenon," the Chilean fisheries institute IFOP said in a statement to AFP.