"However, the beach has very good-quality water for swimming, remembering that young children need to be supervised for safety reasons," he said.
Hastings District Council has put up signs warning against swimming in the Puhokio Stream and is investigating the potential causes of contamination.
Dr Jones said other freshwater bathing areas could also become contaminated following rainfall events.
A quick test to decide whether to swim in fresh waterways, such as lagoons, streams or rivers, was to check whether you could see your feet when knee-deep in the water.
However, for official guidance on where it's safe to swim, people were encouraged to check www.hbrc.govt.nz for the latest water-quality information, he said.