Kapiti Coast District Council is urging people hoping to swim on the coast this weekend to stay out of the water.
Bacteria levels in rivers and streams and beaches are higher than normal.
Environmental standards manager Jacquie Muir says wet weather is to blame.
"With the rainfall, our land's been flushed in a short period of time into our waterways.
"We're researching over the weekend, and on Monday will update our community with the results."
Ms Muir says anyone who goes against council advice will likely pay the consequences.
"Upset stomachs, bacterial infections, staph infections, all sorts of stuff like that."