Cyanobacterial blooms and chlorophyll-a - how to monitor them
In summer, when it turns warm and windless over a lake, a question returns that every bathing-site keeper and every water researcher knows: is this a bloom yet? People who watch the water regularly - monitoring staff, lifeguards, naturalists, lakeside communities - learn to read the early signs: streaks on the surface, a greenish “scum”, a sudden drop in transparency. Their vigilance really matters, because cyanobacteria can produce toxins, and the safety of bathers depends on a sound assessment.
It is a rewarding subject of observation, because it combines simple looking with a concrete measurement - and because it so clearly depends on the weather. Cyanobacteria like warm, calm, sunlit water rich in nutrients. Anyone who monitors them systematically, setting observations against atmospheric conditions, begins to predict the risk instead of merely reacting after the fact. It is very satisfying, useful work.
What and how we observe
Monitoring combines several simple paths:
- Visual observation - streaks, scum, water colour, smell; noted descriptively and with a photo.
- Transparency (the Secchi disk) - a sudden drop can be an early signal.
- Chlorophyll-a - an indicator of algal biomass; measured with a fluorometer in the field or determined in a laboratory (after extraction). Dedicated sensors also detect phycocyanin - a pigment characteristic of cyanobacteria.
What drives a bloom - i.e. why the weather
Cyanobacteria are favoured by: high water temperature, plenty of nutrients (phosphorus, nitrogen), calm and sunny weather, and stratification (no mixing). Wind, in turn, can “push” the scum into one corner of the lake. That is why the measurement gains a lot when you set it against temperature, sunshine and wind - here the weather is a co-author of the result.
How to take the measurement - step by step
- Set up fixed sites (including typical scum-accumulation spots) and a fixed time.
- Note the visual observation (description + photo) and the transparency.
- Measure chlorophyll-a / phycocyanin (sensor) or take a sample for laboratory determination.
- Record the conditions: water temperature, wind, cloud cover - they explain the picture.
- Remember that a bloom can be patchy - wind moves it within hours.
What the result means
Rising chlorophyll-a, falling transparency and intensifying visual symptoms are the picture of a developing bloom. The greatest value lies in the seasonal trend set against the weather: that is when you can see how a run of warm, windless days translates into the water - and you can react in advance.
WHO alert thresholds for recreational waters (Alert Levels Framework, 2021)
| Level | Cyanobacterial biovolume | or chlorophyll-a (when cyanobacteria dominate) | Transparency (Secchi) |
|---|---|---|---|
| Vigilance | 4 mm³/l | 12 µg/l | usually 1-2 m |
| Alert Level 1 | visual entry point: cyanobacteria clearly visible, streaks, turbidity | - | 0.5-1 m |
| Alert Level 2 | 8 mm³/l | 24 µg/l | typically scums where contact happens |
The biovolume and chlorophyll thresholds are derived from the guideline values for toxins - the recreational value for microcystin-LR is 24 µg/l. Chlorophyll-a is a proxy for the toxin that actually matters, so it only works when cyanobacteria dominate the community; with mixed phytoplankton it understates or overstates the risk. Treat a visible scum where people enter the water as a high-risk situation regardless of the measurement.
⚠️ Older material still quotes the thresholds of the 1999 WHO guidance (20 000 and 100 000 cells/ml, 10 and 50 µg/l chlorophyll-a) - that edition has been superseded. WHO moved from cell counts to biovolume, because with small-celled cyanobacteria a high cell count meant practically clean water and led to unjustified bathing-site closures; the 20 000 cells/ml criterion itself is questioned in the new edition. If you see “50 µg/l = moderate risk” somewhere, you are looking at the 1999 edition - today that value is more than twice Alert Level 2.
These are WHO guidelines, a starting point for your own risk assessment - not a legal standard. The decision to close a bathing site is taken by the health authorities under their own procedures, not from a reading on a private sensor.
What you can see with the naked eye - and what it suggests
| Visual sign | Most often | Field test |
|---|---|---|
| A greenish, uniform “scum” | cyanobacteria (e.g. Microcystis) | a stick: it disperses like paint, with no filamentous structure |
| Green, filamentous clumps | filamentous algae (not cyanobacteria) | a stick: it winds onto the filaments, the structure is palpable |
| Fine green “grains” on the surface | duckweed (a plant, not an alga) | individual fronds are visible to the naked eye |
| Yellowish dust on the surface, especially in spring | tree pollen | a glass: it settles, it does not dissolve in water |
The distinction matters in practice: only cyanobacteria produce toxins dangerous to people and animals - filamentous algae and duckweed are an aesthetic problem, not a health hazard. When in doubt, a chlorophyll-a or phycocyanin measurement settles what the eye cannot reliably tell apart.
The most common mistakes
- A single point and time - a bloom is patchy and mobile; measure at several places.
- Skipping the weather conditions - without them the dynamics are hard to understand.
- Visual assessment only - it is worth supporting it with a measurement (chlorophyll/transparency).
How often
In the bathing season and during favourable weather - more often (even several times a week in risk periods), otherwise in a steady rhythm. What counts is the repeatability of sites and time.
Sources and further reading
Monitoring of bathing waters and lake-status assessment is run by public services (e.g. GIOŚ and sanitary-epidemiological stations in Poland); it is also worth reaching for guidelines on cyanobacteria and methods for determining chlorophyll-a. The thresholds in the table above come from chapter 5 of I. Chorus, M. Welker (eds.), Toxic Cyanobacteria in Water, 2nd ed., WHO 2021 - the chapter is openly available: cdn.who.int - chapter 5 (PDF). (Checked 19 August 2026.) ⚠️ The 1st edition of 1999 circulates under the same title - check the year, because the thresholds differ between editions.
📊 See it live: Global Rivers & Lakes Watch - a public dashboard from three stations in three countries: the Maumee River (Ohio, USA), the river Main in Frankfurt and the LéXPLORE research platform on Lake Geneva. Water temperature, dissolved oxygen, pH, conductivity, turbidity and chlorophyll-a are fetched automatically (USGS Water Services, WSV Pegelonline, Eawag Datalakes), with correlation tiles and a station map. No login.
How to make it easier
Bloom monitoring is by nature data from many sources at once: observation, transparency, chlorophyll - plus the weather, without which the picture is incomplete. Combining it all manually is a tedious puzzle.
LimnoLog assembles it into one picture - and here connectors help:
- you record observations and measurements (also your own indicators: visual assessment, chlorophyll, phycocyanin) right in the field, also offline;
- a connector automatically pulls weather data from public APIs (e.g. IMGW-PIB) and saves it alongside your measurements - temperature, wind, sunshine on the same timeline;
- so you see the bloom and the weather together - a run of warm, windless days and the lake’s response form a clear pattern that helps predict the risk;
- you can share the results via a public link (useful for bathing sites and communities) or export them.
The same system covers, alongside cyanobacteria, transparency, oxygen, temperature and any other indicator - a full picture of the lake in one place.
Early users get free access for now and keep their features for good. If you watch over your lake - take a look and try it.
See it in the LimnoLog app
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