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. Hi, would be possible to develop smallish aerators, solar powered, that could be chained together every few meters than can be deployed in places where the water flow has slowed down or is stagnant? I know that some single aerators were deployed in a couple of places but this didn’t make much difference. Was this because there wasn’t enough of them? The idea of chaining a number of smaller units together would incease the size of the area aerated. Solar power could charge up rechargeable batteries to keep the aerators working at night.

    I thought I’d just ask.

  2. maxban1938 says “Our farmers cannot feed the world without a reliable supply of cheap fresh water”
    We should NOT be attempting to feed the world with produce from this – the driest country in the world !
    If a country cannot feed itself then it has grown too large and is not viable in the long term and requires to take suitable corrective action.
    I know that such a Darwinian viewpoint will not find favour with many but as we live in an Darwinian world, I am convinced that it is true

  3. Your article states the area had less rainfall than ever before, but didn’t the Murray dry completely during the Federation Drought?

  4. Another idea to provide addition flushing other than building conventional dams could be to use inflatable weirs which would store and release excess water. They could be inflated by water or air and would be located at logical intervals to provide adequate flushing capacity. They would be designed to store within the safe capacity of river banks so as not to cause adjacent flooding. The weirs would be made of tough, durable, flexible materials like butynol rubber. There may also be some potential for micro hydro power generation on water release or times of high flows. In the event of algal blooms, inflatable weirs could possibly be used contain the spread of blooms and fish deaths with flows supplemented by downstream weirs. Analysis of fish migration, anti puncture design and restrictions to river transport would need to be analysed.

  5. I think approx. 240yrs of white settlement and farming practices have bankrupt the landscapes resilience, ability to cope with droughts. Before we arrived almost everything that grew on the Australian continent died on the continent and was recycled, now we export millions(my guess) of tons of fruit and vegetables plus live cattle overseas and every time we do that we also export all the nutrients and moisture used to grow those items which I believe is unsustainable and an intolerable burden on the Australian landscape. People might make the argument that we also import food but most of that food is consumed in the cities and the human waste generated treated and generally not redistributed over the landscape hence we have a net loss of nutrients and moisture to the landscape.

    I also would like people to consider humanities preoccupation with our own importance on this small green marble called earth. Every time we make decisions in humanities interest with no regard to the impact on other so called lesser species we take a step closer to being the architects of our own extinction, if you give it some thought we are the least necessary species on the planet, except to ourselves, as either no or very, very few other species need us to survive whereas we on the other hand rely on many, many species if not nearly all for our existence i.e. plankton, krill, fish, birds, bacteria, fungi, insects……I think you get the picture.

    The other point is that back around 1880 there were about 1.5 billion, give or take a few million, people on the planet so our impact wasn’t so great, now there are over 7 billion of us and our impact is substantially increased and generally detrimental to the living system called earth.

    I mention these things because I think they are background issues that have led to our present dilemmas, in particular dealing with drought. We think in terms of put a dam here for the benefit of humans or divert water here for the benefit of humans at the expense of the natural environment, thinking these actions will have no impact on the local and wider natural environment, bad idea in my humble opinion as these environmental systems have evolved to be relatively stable for hundreds if not thousands and maybe hundreds of thousands of years and our interference destabilises them.

    Natural lakes, swamp lands and artesian aquifers are like water bank accounts the environment, and us to a limited extent, can drawn on in times of drought but we have almost ruined these in Australia through mismanagement.

    Possibly the floods in northern Queensland are the result of the weather systems instability, but who knows, 240yrs is a blink in terms of ecological evolution. One of the unfortunate side effects is all the man made chemicals and other debris that will have been dumped into the waterways and subsequently the ocean.

    Whether climate change is man made or a natural occurrence it would seem to make sense to try and ameliorate the impact by moving to more sustainable farming techniques.

    I guess recent events are showing us all it is the environment that really has the power.

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