Chances are if you are eating salmon in Japan, the United States, Spain or Brazil, it comes from Chile, the second largest global producer of one the world's most popular fish.

But in Chile, the industry has become synonymous with the massive use of toxic chemicals and antibiotics used in overcrowded fish farms that are destroying the ocean's eco-system in areas further north in Patagonia, where the damage has been well documented.

Now, salmon farmers want to make the Magellan Strait their next main production centre.

There are already more than 100 farms operating there - many in areas declared national parks and reserves, and requests for 342 more concessions are in the works.

Alicia Gallardo, deputy director of the National Fisheries Service, told Al Jazeera that the colder waters of Magellan are better for salmon and drastically reduce the need for antibiotics, though not the pesticides used against sea lice and other pests.

She argued that the service has been introducing more stringent sanitary regulations since the outbreak of a virus in 2007 nearly crippled the industry.

"The future of food production is in the sea, and Chile's responsibility is to produce quality food in quantity in a sustainable way," said Gallardo.

"What we are doing is ensuring food security, and contributing good quality proteins to the world. Our responsibility is to meet not only environmental and sanitary standards, but also social and economic."

But at what price?

While there is still no conclusive evidence, a number of marine biologists believe there could be a strong link between the tonnes of protein waste dumped into the ocean in the form of dead salmon, salmon faeces and uneaten salmon food, and the increased outbreaks in Chile of deadly Red Tide, a highly toxic algae that kills marine mammals, molluscs and fish, including salmon.

"There is a proven relationship between Red Tide formation and ammonia, which is the result of the decomposition of organic matter," said Professor Tarsicio Antezana, a marine biologist and oceanographer.

"When you throw protein, a piece of fish or food into the sea, there will be decomposition and ammonia, and this algae is eager to get ammonia and they are very good at getting this ammonia and blooming."