The naturally occurring bacteria has thrived in the warm weather conditions to overtake waterways stretching from Albury to Torrumbarry Weir, including the Mulwala main canal offtake.

Short-term health effects include gastroenteritis if it the water is ingested and the potential for skin and eye irritation from direct contact.

The algal bloom looks like it will continue for at least the next seven days, which have been forecast for temperatures in the high 30s by the Bureau of Meteorology.

DPI Water acting director water evaluation Allan Raine said, while the department couldn't predict how long it would last, he hoped it would clear by Easter.

“We've got four samples from Lake Hume which are all high alert,” he said.

“Once it gets above a certain biovolume we regard it as potentially toxic.

“It's very hard to predict, the only way it will slow down is if we get sustained cooler weather or some good rain - they are the main two things we are hoping for.”

The last big outbreak of toxic algae in the North East was in 2009-10 when a 1000 kilometre stretch of water was affected.

A powder-activated carbon was used to treat it, helping the cell count to lower just days before the Easter tourism boom.

Albury and other affected councils have put warning signs in place along main entry points to waterways containing the algae.

Mr Raine said communities would be notified as soon as there was a change.

“It’s very difficult for people to determine, I encourage people avoid contact with red alert water,” he said.

“It's usually visible with bright green scum on the surface of the water.

“Under some conditions, with blue-green algae, it can be below the surface of the water and it is more difficult to see – it may look like it's not there at all.”

The bloom began between Cobram and Barmah on February 23 then spread from Lake Mulwala to Torrumbarry Weir.

By February 29 it hit Corowa and, at the beginning of March, the algae headed east to Albury before blooming in Lake Hume on Thursday.

The Murray Regional Algal Coordinating Committee warned algae was not always visible on the water.

Water treatment is in place by local water utilities.

Livestock owners are reminded to continue to check stock water supplies for blue-green algae and to remove stock from foreshores where surface scum is visible or blue-green algae are suspected.