Heavy rain flushed contaminants from urban and rural land into waterways even around sites in Hawke's Bay that have generally good water quality, according to the council.
A HBRC spokeswoman also encouraged the public to use the "rule of toes".
"A handy guide is - if you can't see your toes when standing knee-deep in water, then water quality is not the best for a swim," she said.
Director of lifeguarding at Westshore Nathan Berry said the public should be cautious about getting in the water this weekend – whether in the ocean or a river.
"If you know somewhere and it's changed because of this large water movement just have a think about whether it's actually worth going in," he said.
"I'd be a bit worried about things moving fast in rivers."
In terms of swimming in the ocean, Berry said the biggest concern is the pollution.
Westshore Surf Life Saving Club's usual mid-week trainings on Westshore beach have been moved up the coast, closer to where the water is cleaner.
"I'd be in the water most days, but I haven't been this week because I'm worried about the health risk associated with that," Berry said.
HBRC water quality and ecology team leader Vicki Lyon said their team tests more than 30 popular recreational swimming spots across the region every Monday – from November until mid-March.
"It's important to be aware that our samples were taken prior to the intense rainfall experienced in Napier on Monday, and it is best to avoid these waters until further sampling can confirm that the water quality is suitable for swimming again," she said.
The water quality team is working closely with the national team to feed up-to-date results online at LAWA.org.nz/swim and on to the HBRC website.
"This gives a great picture of weather, water temperature, facilities and how to get to swim spots," Lyon said.
