Rain has washed away most of the toxic algae found in parts of the Hutt River, near Silverstream north of Wellington.
Greater Wellington Regional Council last week warned dog owners about the algae, after it found mats growing on the riverbeds had reached moderate levels.
If ingested, the algae can kill livestock and dogs, and cause vomiting, diarrhoea and skin irritations in humans.
The council's environmental science manager Graham Sevicke-Jones said the amount of toxic algae had dropped since rain at the weekend, and the risk was now low.
However, he said levels could go back up with stable weather.