There are warnings out for a number of other rivers in the Wellington region.
The Waipoua River has been found to be the worst affected in the area, passing the 50 percent alert level, which means swimming is banned.
Council environmental scientist Mark Heath said he had never seen a bloom this widespread.
With no rain in prospect the toxic algal levels were likely to deteriorate further.
"We're advising people to know what toxic algae looks like and if you see it, to avoid it."
Detached algal mats, which can be deadly for dogs, have been seen in all rivers, Heath said.
River conditions will be reassessed tomorrow.
- RNZ