Three streams that children love to play in at Whanganui beaches are unsafe for swimming, Horizons Regional Council science and innovation manager Abby Matthews says.

The three are the Mowhanau, Kai Iwi and Ototoka streams, where children splash and paddle all summer.

Council staff monitor them weekly during summer for bacteria such as the faecal coliform E. coli.

"Monitoring has shown that these streams are generally unsafe to swim in, so we advise against doing so," Matthews said.

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Permanent health risk warning signs are being put up at them by Horizons, in conjunction with Public Health.

Swimming is especially likely to be unsafe if the water is murky or if there has been recent rain, Matthews said.

In contrast, the seawater at Kai Iwi Beach is generally safe for swimming.

In January 2017 temporary warning signs were put up after a power failure to Mowhanau's pumping station resulted in a sewage spill into Mowhanau Stream.

Whanganui District Council was prosecuted for the illegal discharge, found guilty and will be sentenced on November 1.

The pumping station there was upgraded in March last year, so future power failures should not have the same effect.

But run-off from farms also contributes bacteria and nutrients to the streams.

The Mowhanau Stream runs through Bason Botanic Gardens.

In summer, when the weather is warm, its nutrient-rich water grows great mats of weed in a dam there.

Horizons has been working with landowners and other agencies to improve the water quality in the area.

The work has included fencing to keep stock out and protect whitebait breeding grounds, and planting native trees and shrubs to improve native fish habitat.

The council also produces farm plans that help landowners reduce erosion, Matthews said.