The shires of Toodyay and Northam were contacted to erect signs notifying the public of the bloom.
Shire of Northam President Steven Pollard said he had noticed a patch of algal bloom in the Kings Creek drain.
‘I don’t think it’s noticeable near the town. It’s mostly further out,’ Mr Pollard said.
Department staff took water samples from sites along the river last month after reports of concerns about the river’s appearance.
Swan Avon region manager Don Cummins said the analysis identified three species of blue-green algae in the water.
‘The most affected area is from Katrine Pool through to Cobblers Pool,’ Mr Cummins said.
‘The Department of Health advises against recreation in waterways during algal blooms.’
He said the bloom was likely to have been sparked by summer rain bringing increased input of nutrients and organic material from the Mortlock River into the Avon system.
‘Low rainfall and seasonal low flows in the summer months can lead to less dilution of nutrients and, in prone areas, this may lead to increased algal growth.’
Shire of Toodyay President Kevin Hogg described the bloom as a ‘natural phenomenon’.
‘A lot of the water has dried up now. There is not a lot that we can do about it.’
The Department of Water would continue to monitor the situation.