That hasn't happened, Horizons' water quality spokesman Barry Gilliland said, because such spikes can usually be explained by high rainfall in the catchment washing animal faeces into the river.
Or, in this case, it could have been something as temporary as dog poo washed into the river with stormwater.
A bacteria level of 800 on March 16 was easier to explain, because there had been rain on and off for the previous four days.
The samples are taken at the marina's steps, not further out in the flow, where there would be less effect from stormwater.
People need to pick their time to swim in the Whanganui.
Mr Gilliland says it's best to wait two or three days after heavy rain, but water quality at the marina is generally good at high tides, when there is a lot of seawater in.
Overall, and judged on three years' water sampling results, the Whanganui in the city is given an orange light for caution: at times swimming can put people at 5 per cent or greater risk of illness.
E coli bacteria are found in faeces, whether of humans, birds or animals. Health protection officer Margaret Tunbridge said they are not a problem in themselves but can indicate other harmful organisms, such as giardia and salmonella.
In the days when human sewage was in the river, bacteria numbers were much higher.
The Public Health Unit has never had a verified case of illness from people swimming in the river. It would be hard to prove, because there were always other possible sources of illness and testing in the river would have to happen immediately and show the same organisms.
Most people don't report mild stomach upsets anyway.
"I wouldn't ban children from swimming in the river because there might be some risk," Mrs Tunbridge said.
If bacteria numbers are consistently high and health concerns are raised, councils are required to put up warning signs. Such a sign is up at Mowhanau Stream. Toddlers often paddle there and it has consistently high bacteria levels.
The sign recommends people stay out if they have open wounds, keep their heads out, avoid swallowing water, and wash their hands before eating.
Public Health will review this season's water quality sampling with Horizons and Whanganui District Council, Medical Officer of Health Patrick O'Connor said.