The green, slimy bloom stretches from the estuary’s northern end near Cathedral Avenue.

Winds and currents have carried it down towards the waterway’s discovery centre.

Resident George Mardon and wetland ecologist Mike Whitehead believe the algae is due to excess nutrients from the Kemerton Waste Water Treatment Plant.

The plant takes waste water from Australind and Eaton homes and businesses, which is treated and irrigated onto a nearby tree plantation.

Mr Mardon said the bloom was the worst he had seen in the northern end of the estuary in 30 years.

He is worried the bloom will threaten fish, crabs and vegetation.

Mr Whitehead said he came across worrying results in wetlands west of the treatment plant during research.

"What’s the source if (the plant) is not it? Because there is nothing else out east of there" Mr Whitehead said.

"I am more concerned about the implication this has on the whole industrial park as a potential source of groundwater pollution."

Authorities involved with Kemerton deny the algae bloom was caused by nutrients leaching from the plant.

The Department of Environment and Conservation, Department of Water and the Kemerton plant’s lincensee Water Corporation said they were aware of the concerns.

Department of water acting director general John Ruprecht said the algal bloom was investigated and identified as harmless but did appear larger than previous outbreaks on the estuary.

He also said drinking water would not be threatened because the bores where water is gathered from was south of groundwater flow from the plant, which he said flowed west.

Water Corporation regional manager Scott Moorhead said monitoring results indicated there was minimum impact from the irrigation on the quality of groundwater but there had been changes.