Aucklanders have raised concerns events are being "needlessly" cancelled due to an alert system based on weather data rather than water testing.
But Auckland Council says it is the best method available to keep members of the public safe.
Safeswim provides water-quality forecasts and up-to-date information on health and safety risks at 84 beaches and eight freshwater spots in Auckland.
It has three levels: green - meaning low risk and safe to swim, orange - low to moderate risk but still safe, and red - high risk and unsafe for swimming.
It was set up in November by Auckland Council, Watercare, Surf Lifesaving Northern Region and the Auckland Regional Public Health Service, as Aucklanders became increasingly concerned about poor water quality, mostly from storm run-off and sewage overflows.
Takapuna resident Ian Gunthorp said on Tuesday during swimming races at Takapuna beach that Safeswim indicators showed orange for the afternoon and red for the evening.
"At 5.50pm juniors were allowed to swim but at 6.30pm a larger body of swimmers and paddlers were not allowed to race.
"Neither in the intervening period nor immediately prior was there any rainfall or toxic spill and no perceptible change in tide or wind and yet a computer dictated that the surf club support, and therefore the races, had to be cancelled."
Gunthorp has been swimming almost daily for the past 40 years off Takapuna beach and regularly swims with a group.
He had never been sick after swimming in the harbour, although he said that might be because he was lucky.
"Clearly the storm drainage problem has to be fixed, and there is value in a warning system, but what concerns me is a computer is making illogical decisions based on a forecast rather than real data.
"When the model allows a machine to dictate the actions of maybe thousands of people the results can be nonsensical."
Safeswim technical lead Dr Martin Neale said the models were designed in such a way as taking water samples from beaches did not give timely information about water quality, and therefore the health risk that beach users were potentially exposed to.
"As it typically takes around 48 hours to receive water-quality results after collecting and analysing water samples from beaches, using this monitoring approach would mean that the best information we could provide beach users about water quality would be around two days old."
While Auckland was the first region in New Zealand to deploy models this way, it was used internationally, including in Melbourne, Sydney, Hong Kong, Denmark, Scotland and parts of the USA, he said.
"All of the aforementioned use rainfall models as a predictor variable, as it is incredibly important in mobilising and transporting contaminated water to beaches."
The water quality at a location may change some time after it has rained, as the contaminated water took time to travel through the catchment.
"As rain falls in a catchment, it picks up contamination from all the surfaces it flows on, transfers this into the stormwater systems, which transport this water to nearby streams or beaches.
"This process takes time, therefore water-quality changes at a beach may occur some time after any rain has fallen in the catchment.
"The larger the catchment, the longer the time may be before the water quality at a beach is affected by rainfall."
At Takapuna last week, there was a short, sharp rain event around 4pm.
"The model at Takapuna showed that water quality at the beach began to deteriorate almost instantly, but did not breach the guideline values for acceptable swimming until an hour or so later.
"This is why there appears to be a disconnect between the rain falling and the change in water-quality status of the beach.
"We also know that once the water at a beach is contaminated, it will persist for around 48 hours. This is why Regional Councils across New Zealand advise to avoid swimming for up to three days after rain.
"An additional issue that contributed to the unfortunate situation at Takapuna this week was that the rain which fell in that area was greater and arrived earlier than forecast.
"The weather forecast for Tuesday during the day showed rainfall arriving around 7.30pm, but in reality it arrived around 4pm.
"The Safeswim models are hooked up to real time rainfall monitoring and re-calibrate as this data becomes available.
"This is why the water-quality information for Tuesday changed during the course of day."