Many of Auckland's most popular beaches aren't safe to swim at for the next 24 hours due to faecal bacteria contamination.

Alerts on the SafeSwim website have deemed the beaches - including Milford, St Heliers and Mission Bay - as "high risk" until Wednesday evening.

This is because of the storm set to lash the country this afternoon and standard advice is to avoid swimming at the beach 48 hours after heavy rain.

Torrential or heavy rain can overwhelm wastewater networks by stormwater and groundwater, leading to sewage overflows which drives more diffuse pollution into the ocean.

Some of the beaches with a "high risk" warning in place include:
• Mission Bay.
• St Heliers.
• Judge's Bay.
• Milford.
• Narrow Neck.
• All the East Coast beaches.
• All the beaches on and near the Whangaparoa peninsula.

The SafeSwim website, run by Auckland Council, says its models are predicting the levels of faecal bacteria exceed national guidelines at the beaches.

Most water-quality problems at Auckland's beaches stem from animal or human faeces, which can foul water with disease-causing bacteria, viruses and nasty bugs like salmonella, campylobacter and giardia.

The warnings come as a massive Tasman low moves over New Zealand, bringing rain to 90 per cent of the country.

Heavy rain watches are in place for the Bay of Plenty, the Central Plateau and Taranaki.

The high-risk warnings for Auckland's beaches are set to lift on Wednesday evening.