Auckland's St Mary's Bay is out of action for swimmers, just one of a number of holiday hotspots deemed unsafe.
Wastewater overflow has been detected at the inner-city Auckland bay, according to Land Air Water Aotearoa (LAWA) and Auckland Council.
The council's Safeswim site shows a range of spots are suffering poor water quality, including Cox's Bay, Taumanu East, Green Bay, Wood Bay, French Bay, Armour Bay, Fosters Bay, Piha South and North Lagoons, Bethells Lagoon, Te Atatu Beach, Meola Reef, Weymouth Beach, Little Oneroa Lagoon and Takapuna Beach.
Down south there is a toxic algae alert in the Hutt River.
"There continues to be large amounts of toxic algae breaking free of the riverbed, floating downriver and accumulating on the river margins," LAWA says on its site.
"Thus, the risk of accidentally swallowing toxic algae, while swimming, remains high."
Small amounts of toxic algae have been measured at the Wainuiomata River and Waipoua River, but at safe levels.
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Most beaches and swimming spots around the Wellington region are safe according to LAWA, though caution is advised on the Waikanae River and Hokio Beach. The Makakahi and Kaikokopu streams are deemed unacceptable however.
There are a number of spots in-between Auckland and Wellington deemed unsafe, including Waihi Beach at 3 Mile Creek, Sunset Beach at Port Waikato, the Rere Rockslide on the Bay of Plenty's Wharekopae River, Mangawhero at Ruakawa Falls, the Whanganui River at Pipiriki, Wardlaws Glade near Whakatane and Hautapu at Papakai Park, near Taihape.
In the north, the Hatea River at Whanganui Falls has shown high readings of E. coli - most other spots are just fine.
In the South Island, caution is advised for swimmers taking to the waters at Lyell Creek and Lake Hood.
Waters to avoid entirely include the Kaiapoi River near the boat ramp in the township, the Avon River at Kerrs Reach, the Selwyn River at Coes Ford, the Kakanui River at Clifton Falls Bridge, Lake Hayes at Mill Creek Shadows and Lake Tekapo at Camp Beach.