We explore the science behind the recent toxic algae outbreak and the mass fish loss in the Murray Darling, and look at ways to manage it in the future.
A mass amount of dead fish washed up on a river bank.

CSIRO expert Dr Klaus Joehnk says that high temperatures and dry conditions associated with heatwaves will continue to create ideal conditions for blue-green algae. Credit: Facebook/Debbie Newitt/ABC.


Have you seen the distressing videos and images of mass fish deaths in the news over the new year? In the past month, it has been estimated up to a million fish have died along a 40-kilometre stretch of the Darling River in far west New South Wales.

Blue-green algae has been identified as the primary cause and the dead fish have included native species such as bony bream, Murray cod, and golden and silver perch.

In addition to the distressing loss of fish, news articles have advised people not to swim or drink contaminated water in ‘red alert’ algae areas and farmers have been asked to find alternative water sources for livestock.

Hearing from an ecosystem expert

We sat down with our blue-green algae and freshwater ecosystem expert Dr Klaus Joehnk to discuss the science behind the recent toxic algae outbreak and the mass loss of fish.

A middle aged man wearing a red jacket, standing outside surrounded by gum trees.

According to Klaus, the severe blue-green algae outbreak resulted from a combination of factors, including drought and heatwave conditions, and no water flow.

Why do we get blue-green algae outbreaks?

Every year in the summer months Australian waterways regularly experience the occurrence of blue-green algae (cyanobacteria) outbreaks. Warm, slow moving or stagnant water, high solar irradiance (direct sunlight or lack of clouds) plus plenty of nutrients are the perfect conditions for algae to grow. As these algae start dying there is a rapid decline in dissolved oxygen in the water due to decomposition to levels that can lead to fish deaths. Deaths can be extensive when fish cannot move to safe spots or artificially created refuges.

Why was the outbreak so severe in the Murray Darling Basin?

It is likely the fish kill was a combination of factors:

  1. Drought conditions leading to stagnant water in the region which has received less rain than ever before in some parts, (see Bureau of Meteorology rainfall deficiency map here)
  2. Development of an extensive and concentrated blue-green algae bloom due to heatwave conditions, no water flow, and nutrient concentrations in the water due to a range of human-derived and natural inputs.
  3. The sudden passing of a cold front, leading to water mixing bringing up anoxic (deoxygenated) water.
  4. With the water column (from river surface to riverbed) experiencing low oxygen levels, fish had no refuge to swim to, and thus died.

What’s next?

Can the Murray Darling Basin expect more blue-green algae as summer continues?

Unfortunately yes. High temperatures and dry conditions that come with heatwaves also mean an increase in water temperature and continued ideal conditions for blue-green algae. The decaying dead fish are also contributing to lower water quality and less oxygen in the water.

Menindee from above: a satellite image from the day before the disaster, 4th January 2019. Generated with Google Earth Engine using free Sentinel 2 satellite data.

What are the options for management and control of blue-green algae?

Our water scientists have a long-standing active program building up an understanding of the complex chain of events that leads to an algal bloom, and the aftermath of toxins released into the water.


  • We are developing short-term forecasting capability to predict cyanobacteria bloom development on a short, seven-day term. This is based on remote sensing and models.
  • Fast and cost-effective assessments of water quality, such as on-ground and satellite remote sensing approaches, as well as more continuous monitoring systems can be used to assess the conditions of our inland water. This can identify and predict potential changes in water quality in response to changes due to outside influences, such as land use changes, flooding, fires, and climate. We have already been investing in the development of these monitoring systems in some parts of the basin.
  • We are also working on physical, biological and nutrient controls to manage the algae.
  • We are continuing to work with state and federal agencies, including with the Murray-Darling Basin Authority (MDBA), to support the MDBA’s modelling and forecasting work in relation to water management and planning.


  1. Hyacinth is a problem floating weed but is much easier to control than algae. It not only removes nutrients but also heavy metals. It also has the advantage that it can be confined by a simple floating rope and is also easily harvested

  2. I think that Max Bancroft has hit the nail on the head when he mentions the suggestions of J A Bradfield. These were still talked about when I arrived in Australia in 1952. The idea was to repeat the snowy mountains scheme with the frequently flooding East Coast rivers. Not only would this bring water to where it is needed most, but it would also increase substantially our supply of non- fossil fuel burning electricity, instead of wasting huge amounts of money on unreliable sources such as wind and solar. We need more than more accurate ways of viewing and measuring disasters, even if these actions create a host of pleasant committees and research. We need positive action for prevention.

  3. Where are the nutrients, mainly phosphorus, for the algae coming from? If we can prevent the algal blooms then maybe we can lessen if not prevent the fish kills.

  4. The causes of toxic blooms are well known. We can’t control drought but we can go some way to eliminating causes. Even in stagnant pools and dams, mechanical circulators can pump oxygen-rich water from the surface to the lower levels. Maybe filters on the intakes to these circulators could filter out blue green algae before they bloom, so non-toxic green algae gain a competitive advantage in nutrient uptake..

  5. Hi,
    The ‘normal’ conditions assumed in the Basin Plan and other management response designs is the large weakness. As climate variability increases and water extractions become more intense – through farm water storages and improved on-farm water efficiencies – less will flow into the waterways during dry years, which comes more regularly. Unless we change our management philosophies sadly these events relating to environmental dysfunction will likely to come more often. Of course as fish stocks deplete and the predator-prey relationships alter to the detriment of biodiversity, the magnitude of fish kills could decline.

    Nice work on satellite mapping!

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