Factsheet: Cyanobacteria

Cyanobacteria (commonly known as blue-green algae) are microscopic organisms that play a very important role in many land and aquatic ecosystems.


What are cyanobacteria?

Cyanobacteria (commonly known as blue-green algae) are microscopic organisms that play a very important role in many land and aquatic ecosystems. In aquatic environments cyanobacterial cells can multiply and form blooms in the river (planktonic) or dense mats on the river bed (benthic). Planktonic blooms are generally found in slow moving aquatic systems such as lakes while benthic blooms usually occur in rivers.



A colony of Microcystis made up from 100 000s of cells.

Why can extreme levels of cyanobacteria be a problem?

Cyanobacteria inhabit all natural waters and usually only become a problem when they increase to high concentrations, forming ‘blooms’. Cyanobacterial blooms have been a regular occurrence in many New Zealand lakes since the 1970s. However, the frequency of blooms has increased in recent decades which can be linked to higher levels of nutrients in the water as well as climate change.

Other than the general effects of algal blooms on aquatic ecosystem (e.g., reduction in dissolved oxygen and light in the water column), an increasing number of cyanobacterial species are known to produce  poison or toxins. These natural toxins, known as cyanotoxins, can be a threat to humans and animals if consumed in drinking water or by contact during recreational activities. The effect of cyanotoxins varies from rapid onset of nausea and diarrhoea, to, in extreme cases, more serious effects such as liver damage.

Dog deaths associated with benthic cyanobacteria have become increasingly common around New Zealand. In most instances these deaths have been associated with dogs eating a mat forming cyanobacteria called Phormidium. Phormidium mats produce a deep earthly odour that dogs seem to be attracted to. The risk to dogs is greatest when Phormidium mats become detached from the river bed and collect at the river edge where they are easily assessable.

  Phormidium 1Phormidium 2

Phormidium is an example of a cyanobacteria species that can produce cyanotoxins and has been responsible for over 70 dog deaths in New Zealand in the last decade.

How to sample cyanobacteria and which unit are they measured in?

Blooms are much more common in summer than in winter months. Therefore, this is when routine council monitoring should occur and recreational users need to be particularly cautious.

Benthic cyanobacteria in New Zealand rivers are distinctive for their black/blown/green mats often with visible air bubbles and pungent deep earthly/musty odour. Planktonic cyanobacteria in New Zealand lakes and ponds form visible green scums at the water surface. 

 Planktonic bloom

A planktonic cyanobacteria bloom in Lake Horowhenua

Benthic cyanobacteria attached to the river bed are visually assessed with an underwater viewer and percentage cover is recorded (see pictures below). In addition, the river edge is scanned for detached mats that may have collected at the river margins. Recreational users and animals have an increased risk of coming in contact with detached mats.

percentage cover Periphyton viewer

Examples of how to determine percentage cover of benthic cyanobacteria and what an underwater viewer looks like.


Average percentage cover results for each site should be interpreted using a so called “alert-level framework” and the appropriate actions taken (https://www.mfe.govt.nz/publications/fresh-water/guidelines-cyanobacteria/section-3-guidelines).

Planktonic cyanobacteria are assessed by collecting a sample of water from the surface and counting the number of cells present. Similar to mat forming cyanobacteria, planktonic cyanobacteria cell counts should be interpreted using an alert-level framework and the appropriate actions taken.

Where do I find more information?