Cyanobacteria (blue-green algae) and water quality

​Cyanobacteria (blue-green algae) are a type of microscopic, algae-like bacteria which inhabit freshwater, coastal and marine waters.

Cyanobacteria photosynthesise like plants and have similar requirements for sunlight, nutrients and carbon dioxide to grow and produce oxygen. There are many different varieties of cyanobacteria. While often a green or blue-green colour, they can also be white, brown, blue, yellow-brown, or red.

If conditions are suitable, cyanobacteria can increase to excessive levels and form visible ‘blooms’ which can lead to poor water quality and the potential for toxicity.

Cyanobacteria can cause environmental problems, disrupt drinking water supplies, recreational activities and water-dependent industries, and pose a risk to livestock, wildlife and human health.

Black Swan (Cygnus atratus) swimming in a blue-green algal bloom in Lake Burley Griffin, Australian Capital Territory.
Lake Burley Griffin, Australian Capital Territory. Bruce Gray, Department of the Environment and Energy.

Conditions that lead to cyanobacterial blooms

Cyanobacteria can reproduce quickly in favourable conditions, where there is:

  • abundant sunlight
  • still or slow-flowing water
  • sufficient levels of nutrients, especially nitrogen and phosphorus.

In still conditions, surface water may form a separate warm top layer (stratification) in which cyanobacteria is able to access sunlight and nutrients. If these combined factors are present for several days, cyanobacteria multiply and form large ‘blooms’.

Nutrients are either naturally present in sediments or are washed into water systems from external sources. In particular, phosphorus may be stored in significant amounts in sediments and released by normal bacterial activity.

External sources of nitrogen and phosphorus are:

  • agricultural fertilisers
  • household products
  • sewage effluent
  • stormwater runoff.

All of which can enter receiving waters either directly or during rainfall events. The availability of varying levels of nitrogen and phosphorus can influence which species of blue-green algae dominate and form blooms.

Blooms can form in response to increased temperatures and phosphorus levels even if nitrogen in water remains low, as some blue-green algae species can obtain nitrogen from the atmosphere.

Quick fact

Excess nutrients causing rapid growth of aquatic plant and bacterial life in a water body is a process known as ‘eutrophication’.

Effects of cyanobacterial blooms

Cyanobacterial blooms lead to deterioration of water quality and production of toxins by some species. Exposure to algal toxins has been linked to fatalities of livestock, wildlife and pets.

Decaying algae can reduce dissolved oxygen levels in the water column which can severely degrade aquatic ecosystems and lead to the death of aquatic organisms and a decline in biodiversity.

Economic consequences of cyanobacteria outbreaks can arise from restrictions on the consumptive use of water and recreational activities due to health and aesthetic concerns.

Some species of cyanobacteria can produce:

  • allergens or irritants to the skin and eyes
  • compounds that affect the taste of water and produce unpleasant odours
  • hepatotoxins, which damage liver cells
  • neurotoxins, which damage nerve cells
  • cylindrospermopsin, which can damage the liver, kidney, gastrointestinal tract and blood vessels.

In severe cases, the toxins can cause damage to the liver and nervous system and there have been human deaths associated with non-routine exposure to algal toxins through dialysis.

Managing cyanobacterial blooms

The most effective method of preventing cyanobacterial blooms is to minimise the nutrient load entering waterways through:

  • appropriate treatment and disposal of stormwater, agricultural, industrial and sewage effluent
  • planting or maintaining riparian vegetation
  • soil conservation and flow manipulation to prevent the build-up of blue-green algae.

Cyanobacteria management response cycle

Blue-green algae management response cycle: Monitoring regime, leads to, blue-green algae bloom is detected, leads to, alert is triggered, leads to, public warnings are issued, leads to; water and/or equipment are treated: chlorine, coagulation, filtration, leads back to monitoring regime.

In reservoirs used for drinking water supplies, various mechanical methods are often used to mix water and prevent conditions of stratification which could bring about cyanobacterial blooms. Larger water supply authorities generally conduct regular water sampling which allows the public to be quickly notified of any potentially harmful blooms and to obtain drinking water from alternative sources.

Unfortunately, once a bloom is detected there are currently few ways to disperse it without adverse side effects.

Flushing the water body by adjusting river flows may disperse the blooms and break up stratification. The amount of flows needed to disperse algal blooms are not always available and toxins can still remain in the water column, even when algae are not visible.

Boiling water does not destroy algal toxins and can release more toxins as the cyanobacteria are killed.

Use of algicides to control blooms is not recommended by government agencies and is only used in emergency cases.

When a bloom is detected:

  • alternative sources of water should be sought for human consumption and domestic purposes until specialised treatment processes can be introduced
  • comprehensive monitoring programs and emergency plans can reduce effects of the bloom
  • irrigators are usually advised to avoid using contaminated water on edible crops or, if this is not possible, to avoid direct spraying.

National strategy and guidance

The Australian Government cooperates with state and territory agencies to provide policy guidance on controlling cyanobacteria outbreaks.

The National Water Quality Management Strategy (NWQMS) is endorsed by all states and territories and provides guidance on blue-green algae monitoring actions, alert systems and treatment options.

Cyanobacteria is also controlled indirectly through delivering water back into the environment, investing in effective stormwater management and minimising nutrients entering waterways.

Resources for managing risks associated with blue-green algae:

Regional approach

Algal blooms are most effectively managed at the local level because of the varying conditions and circumstances in each case.

Local councils and state water authorities are best placed to investigate suspected outbreaks and alert the public of any unsafe waters.

Regional resources:

Murray-Darling Basin

Managing blue-green algae blooms in the Murray-Darling Basin is a high priority, due to the risks cyanobacterial blooms pose to human health, the environment and the economy.

Release of environmental water at appropriate volumes and times can:

  • help reduce the likelihood and extent of algal blooms
  • maintain water flows in summer months when conditions are most favourable for cyanobacteria.

The Murray-Darling Basin Authority is working closely with the relevant states and territories to implement the Murray-Darling Basin Plan, which aims to return more natural flow regimes to the system.

Water reform in the Murray-Darling Basin is supported by the acquisition of water entitlements, with the objective of returning more water to the environment. These entitlements become part of the Commonwealth environmental water holdings and are managed so that increased flows are provided to rivers and wetlands.


Bacteria: single celled micro-organisms. Most are harmless and very important to the environment.
Dissolved oxygen: form of oxygen in water which aquatic organisms are able to breathe through specialised respiratory systems.
Ecosystem: specific composition of animals, plants and micro-organisms which interact with one another and their environment.
Eutrophication: process where an accumulation of nutrients in water bodies leads to rapid growth of aquatic plants.
Nitrogen and phosphorus:​ chemical nutrients essential for growth, added to many fertilisers.
Stratification: formation of separate water layers.