Authorities are investigating whether negligence at wastewater treatment plants was to blame after millions of fresh water fish locally known as "popocha" began to float up in the Cajititlan lagoon last week.
Some 130 fishermen from the town of Tlajomulco continued to pull dead fish out of the water on Monday and buried them in pits, removing some 53 tons so far, according to the Jalisco state environment agency.
"We don't want this problem to worsen because we would end up in the street," said Rigoberto Diaz, a local fisherman who fears that other species such as tilapia, which unlike popocha is edible, will die too.
Fellow fisherman Mauro Hernan echoed concerns that authorities have yet to confirm the cause of the die-off.
"We were told that the state government will support us. We don't know when we will be able to fish again," Hernan said.
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Jalisco state environment secretary Magdalena Ruiz said it was the fourth unexplained fish kill at the same lagoon this year.
"You can't deny that there's a contamination" due to suspected negligence at wastewater treatment plants, she said Monday.
Authorities are conducting tests on the dead fish while state environmental prosecutors are investigating local wastewater treatment plants.
Ruiz Mejia had said Sunday that such deaths were "more and more" frequent due to "bad management of the body of water."
The Tlajomulco municipality, however, said the deaths were due to a cyclical change in water temperature that caused oxygen to drop.
The local fishermen agree with town officials, saying that other fish species would have been killed if it was a case of contamination.
In a separate incident in July 2013, some 500 tonnes of fish died in a Jalisco reservoir after a company that made food for livestock without a permit dumped huge amounts of molasses into the water.
