More than 32 tonnes of fish were cleared from the Lagoa Rodrigo de Freitas in April and while some contend they were killed by a drop in water temperature, others suggest it was the pollution that proved fatal.
"We have been there a few times and yeah, it's not clean water," high performance manager Alan Cotter said before the New Zealand team departed on Friday for a trip to Europe, which culminates in the world championships in France.
"You wouldn't go swimming in it, but FISA, the governing body, are all over it.
"If they had any concerns they would let us know. They're making sure that it's safe for all our athletes."
Cotter said the big issue with any possible pollution at the venue during the Olympics would be ensuring that even the most innocuous cut or scratch was treated by the team's medical staff to lessen the risk of infection.
Despite the concerns over the pollution, Cotter's preparations for Rio were well advanced with the team's 'day house' already established about two kilometres from the venue.
A day house was used at the Eton Dorney venue for the London Games, where New Zealand won three gold and two bronze medals, to give the rowers a chance to rest between training and races instead of going back to the athletes' village.
Two chefs will also be flown to Rio for the Games to provide the team with their own food.
"The set-up we had in London we are trying to replicate in Rio," he added. "We're trying to make it like New Zealand."
The logistics of getting the team from the athletes' village to the venue and day house will also be tested in August, when Rio hosts the junior world championships.
The senior team will also send 11 athletes and three coaches to Rio after their own world championships, which are from Aug. 30-Sept. 6 in Aiguebelette, to ensure the planning is on track.
Despite all the planning and monitoring of concerns over pollution, however, Cotter said what mattered most was how the athletes performed when they needed to from Aug. 6-14 next year.
"In reality a course is a course. There's a start line and finish line," he said.
"And it's still 2,000 metres long."
(Editing by Nick Mulvenney)
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