Cyanobacteria (Blue-Green Algae) in Inland and Inshore Waters: Assessment and Minimisation of Risks to Public Health

Guidance to Directors of Public

Health, to Heads of Environmental Health in Local Authorities (LAs), and to others in

Scotland, on possible risks to public health of cyanobacteria (blue-green algae) in inland

and inshore waters. It updates previous guidance under the same title that was published

by the Scottish Government Health Directorate previously in 2002, and revised in 2007.




Scottish waters can support numerous different species of algae which can "bloom", either as individual species or in combination, when suitable ecological conditions occur. Some ("planktonic") species exist as single cells or colonies or chains of cells suspended in the water, whereas other ("benthic") species may grow on the sediment along the shallow margins of waterbodies and occasionally form thick, slimy attached or detached mats.

When blooms of planktonic cyanobacteria occur, it is often possible to see colonies of algal cells in the water column with the naked eye. These may resemble fine grass cuttings or take the form of small irregular clumps or pinhead-sized spheres. These colonies can concentrate on a downwind shore and sometimes accumulate to such an extent as to form a "scum" which is a thick (often many centimetres) layer of cyanobacteria. They may also be seen in rivers or streams downstream of lochs.

When the cyanobacterial cells start to die and break up, the toxins which they may contain are released into the surrounding water. Cell pigments are also released resulting in a scum resembling turquoise emulsion paint spilt along the shore. It is important to note that not all cyanobacteria are blue-green. They can range from black through dark brown to khaki, green to blue, and dark red. Decaying cyanobacteria can appear sky-blue, grey, and white.

There are only a few other types of algae (e.g. harmless Euglena, Botryococcus) that will occasionally form scums which can be confused with cyanobacterial scums. Growths of some aquatic macrophytes, particularly duckweed (Lemna), and filamentous algae are also commonly mistaken for cyanobacterial scum by inexperienced observers.

Benthic cyanobacteria can be found in both standing and running waters. The algal mats (biofilms) that these occasionally form can become a problem if the water level drops and exposes the mat, or in some cases, they may detach from the bed, rise to the surface and may then be washed up on the shore. These detached mats are often very different in appearance to planktonic forms. They are usually very dark in colour (black, dark brown or dark green). They are much more cohesive in nature than planktonic scums and can be mistaken for sewage or cow dung. For example, a planktonic scum will flow into a bottle as a liquid whereas benthic scum will be lumpy and often have to be scooped into a bottle or jar.

Sampling equipment

Cyanobacteria can be sampled easily and cheaply using simple equipment comprising:

  • Sample bottles of suitable size e.g. 1 litre plastic bottle for planktonic forms; vials or jars minimum size 30 ml for benthic forms
  • Plastic bucket tied to a rope (optional)
  • Field data sheets or notebook
  • Self-adhesive labels or waterproof marker
  • Preservative (Lugol's iodine) if available can be added to a second sample bottle, which may be necessary only if it is likely that the samples will not be analysed within 24-48 hours. However, Lugol's iodine should not be added to samples if these are required for toxin analysis, since it rapidly destroys the toxins
  • Picnic-style insulated hamper box with chiller packs, to keep samples cool if transportation delays are expected

Sampling health and safety

Cyanobacteria may produce toxins hazardous to human health. Care should be taken to avoid ingesting or coming into direct skin contact with cyanobacterial scum and mat material. Wear wellington boots and suitable waterproof gloves and thoroughly wash hands before eating or drinking.

Lugol's iodine is a skin irritant and is harmful if ingested in quantity. Eye protection and suitable rubber gloves must be worn when handling this chemical. The preservative should be added in a well-ventilated environment.

Normal health and safety precautions should be taken for working in or near water (with specific regard to information, instruction and training, avoidance of working alone, ensuring communications in case of emergency, wearing a life jacket and suitable clothing).

Sampling procedure

Samples are normally collected from a point on the downwind shore of a waterbody where the concentration of cyanobacteria is greatest. This may not be obvious to the naked eye, in which case any suitable site on the downwind shore can be selected. Bear in mind that cyanobacteria will often collect in sheltered bays and inlets. If the downwind shore is inaccessible, then the waterbody should be sampled at the nearest accessible point to the downwind shore and this should be noted on the field data sheet or in a notebook.

In large lochs or inshore waters it is usually impractical to examine the whole downwind shore, in which case one or more samples should be taken at selected points.

Planktonic cyanobacteria or benthic scums are sampled at or just below the water surface, preferable by taking a sample with a bucket and transferring the cyanobacteria or scum sample into a pre-labelled bottle, or by directly immersing a pre-labelled bottle and filling it completely. Occasionally it may be difficult to reach open water, for example, because of dense emergent vegetation. In such cases a bucket on a rope may be a useful aid. Benthic cyanobacteria which might be attached to sediment or stones or have become detached may need to be scooped into a wide-mouthed jar. If water levels have fallen, scums and mats may be stranded on the shoreline and scooped or scraped directly into a container.

The following information should be recorded on the sample bottle label:

  • Name of waterbody
  • Waterbody code (from, available for the larger waterbodies only
  • Sample identifier (site name or number)
  • National grid reference of sampling site
  • Date and time of sampling.
  • Name or initials and contact details (telephone or email) of sampler

Additional information useful to the analyst should be recorded on a field data sheet or in a notebook or communicated via email or telephone. This should include:

  • Sampling location. For waterbodies which are sampled regularly, it may be more convenient to include an outline map on the field sheet so that the position of the sampling site can be marked on
  • The presence and extent of any cyanobacterial scum or mats. For small easily surveyed waterbodies an estimate of percentage cover of the water surface or shoreline could be made or the position of any scum or mat could be drawn on an outline map
  • The presence of any visible cyanobacterial growths in the water column
  • The direction and strength of the wind

Sample handling

Samples should be kept in cool, dark conditions, e.g. in an insulated picnic style hamper box, containing chiller packs, and transported to the laboratory as quickly as possible. If this cannot be achieved within 24 hours then aliquots of the samples should be preserved for microscopy by adding Lugol's iodine solution (note previous Health and Safety instructions). Sufficient should be added to turn the sample a dark straw colour.

Samples for toxin analysis should be stored in a cool box after collection and transferred to a refrigerator at about 4°C, but not frozen, if analysis is possible within 48 hours. If not possible within this period, samples for toxin analysis should be deep-frozen.

Sample analyses

Where appropriate capability exists, samples can be analysed locally. Alternatively, (as indicated in Section 5) various organisations including SEPA and Scottish Water can provide an analytical service to identify and quantify algal blooms in samples taken by others.

Standard operating procedures are used to quantify the type of cyanobacteria present, and cyanobacterial abundance is compared against WHO guidance levels. The identification of dominant cyanobacteria will be to genus level as a minimum requirement and to species level wherever possible.

Toxicity assessment and toxin analysis (see Annex C) testing may be carried out as a further aid to the management of algal blooms or scum on waterbodies with high recreational amenity value or on waterbodies used to supply potable water.

Further information

Further information and advice can be obtained from Ecology staff at SEPA Regional and Area offices. Contact details are given here in Annex C.


Email: Janet Sneddon

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