Tons of dead fish have been removed from a Rio de Janeiro lagoon where Olympic events are to be held in 2016, sparking debate among officials and scientists over what caused the mass die-off, as well as fears that the water may be unsafe for athletes.

Eco-boats commissioned to clean the lagoon have already collected more than 50 tons of dead twait shad, a small silvery fish, NPR reported from Brazil on Tuesday, and were still collecting more.

The die-off took place in Rio’s Guanabara Bay, where Olympic sailing and rowing events are slated to be held in August of next year. Some athletes who plan to compete in the water events have voiced health and safety concerns over the waters.

The die-offs are becoming a common occurrence in Rio, where rivers, lakes and even the ocean are blighted by raw sewage and garbage. Officials have argued over the cause, with Rio’s environmental secretariat insisting last week that the incident is the result of the sudden change in water temperature.

“The intense rains that happened last week and a rise in the sea levels led to a spike in the [sea] water entering the lake, causing a thermal shock,” the secretariat said in a statement, adding that the water temperature had fallen by 7.2 degrees Fahrenheit in a short period of time.

Many scientists disagreed with that explanation, pointing to pollution instead.

The lake “has large concentrations of sulfur because of the organic material dumped into it, and depending on the winds, that material rises to the surface and kills fish,” said Estefan Monteiro de Fonseca, an oceanographer at the Fluminense Federal University.

Cristina Castelo Branco, an associate professor of aquatic ecology at the Federal University of Rio de Janeiro, also attributed the fish deaths to pollution, but in a different way.

Castelo Branco said that pollution from fertilizer, wastewater and storm-water runoff is affected by sunlight, warm temperature and slow-flowing water to produce algal blooms. The algae sucks out oxygen from the water, leading to fish deaths.

“This is a stressed lagoon. We have some problems with oxygen,” Castelo Branco told NPR.

Algal blooms have also caused toxicity levels to spike, which could harm people exposed to the lagoon’s waters, Castelo Branco added.

When toxicity is high, “you cannot swim in the lagoon in that situation,” she said.

Rio’s water quality has become one of the most contentious issues heading into the 2016 Olympics.

Authorities have long said that the games would be the catalyst for a major cleanup of the city’s waterways, but as the showcase sporting event approaches with few improvements, authorities are now admitting that many of the Olympic promises won’t be met.

Rio Governor Luiz Fernando Pezao acknowledged last week that “there’s not going to be time” to finish the cleanup ahead of the games, suggesting it might wrap up by the end of 2018 instead.

Fonesca, the oceanographer, warned that if another fish die-off occurs during the games, “Rio’s image could suffer irreparable damage.”

Al Jazeera and wire services