Freshwater Ecology & Watershed Research

Cyanobacteria · Chapter 5

Harmful Algal Blooms

Full text About 30 minutes Last reviewed 2026-11-05

Safety first If water has a surface scum, looks like spilled paint or pea soup, or has floating or detached mats: keep people and pets out, do not touch it, and do not collect it without an approved protocol. Check current Kentucky HAB advisories (opens in a new tab) before any lake or pond visit. If a person or animal becomes ill after contact, contact a physician, veterinarian or Poison Control.

Learning objectives

After studying this chapter, you should be able to:

  1. Define a bloom and explain why bloom, harmful bloom and toxic bloom are different claims.
  2. Compare microcystins, anatoxins, cylindrospermopsins and saxitoxins by target and producer.
  3. Distinguish intracellular from dissolved toxin and explain why it matters for sampling and treatment.
  4. Explain why cell counts, color and toxin concentration are related but not interchangeable.
  5. Find and interpret current Kentucky advisories and U.S. EPA guidance values.

"Harmful algal bloom" is one of the most-used phrases in freshwater science and one of the most misunderstood. A bloom is a lot of cells; a harmful bloom is one that causes harm; a toxic bloom is one that contains toxins at concentrations that matter. Those are three different claims, and each requires its own evidence. This chapter separates them, describes the major cyanobacterial toxins, explains why the numbers you might measure — cell counts, color, pigments and toxin concentrations — are related but not interchangeable, and shows how health agencies, including Kentucky's, turn measurements into advisories.

5.1What is a bloom?

A bloom is a rapid increase in the biomass of phytoplankton or attached algae, often to the point that it changes how the water looks: green, blue-green, brown or red discoloration, floating flecks, surface scums, or mats on the bottom or shoreline [1, 2]. There is no single universal threshold — scientists define blooms using cell counts, biovolume, chlorophyll or visual criteria, depending on the purpose. In fresh water, most problematic blooms are formed by cyanobacteria, which is why "cyanobacterial harmful algal bloom" (cyanoHAB) is often used, even though cyanobacteria are not algae [3].

Planktonic blooms develop when cyanobacteria grow faster than they are lost to grazing, sinking, flushing and death. Warm temperatures, nutrient enrichment, calm stratified water, long residence times and abundant light all push the balance toward growth, and buoyant species can concentrate at the surface in calm weather [4, 1, 5]. Chapters 3 and 4 develop these drivers.

5.2Why some blooms become harmful

A bloom becomes harmful through one or more of these routes [3, 1]:

  • Toxins. Some strains produce compounds that damage the liver, nervous system or other organs of animals and people (Section 5.4).
  • Oxygen depletion. Dense blooms produce oxygen in daylight but consume it at night, and when a bloom dies, bacterial decomposition can strip oxygen from the water, killing fish and invertebrates (Section 5.6).
  • Taste and odor. Compounds such as geosmin and 2-methylisoborneol give drinking water an earthy or musty taste, increasing treatment costs even when no toxin is present [6].
  • Ecological and economic losses. Blooms shade out other producers, provide poor food for grazers (Chapter 6), close beaches, and reduce recreational and property value. One national estimate put the potential annual cost of freshwater eutrophication in the United States in the billions of dollars [7].

5.3Toxin-producing and non-producing strains

Toxin production is a property of genotypes, not species. Within a single Microcystis population, cells that carry the genes for microcystin synthesis grow alongside cells that do not, and the two cannot be told apart by appearance [8, 9]. Studies that measured toxin genes directly found that the abundance of toxic genotypes predicted microcystin concentrations better than total cyanobacteria, total Microcystis or chlorophyll [10]. And because bloom communities often contain several genera, a bloom dominated by one genus can contain toxins made by another [6].

Rule used throughout this portal Toxin production is never inferred from microscopic appearance, color or the genus present. It is reported only when a toxin has been measured by an appropriate method.

5.4The major cyanotoxins

Cyanotoxins are grouped by the organ or process they target. Four groups dominate freshwater monitoring [11, 12, 13]:

Table 5.1. Major cyanotoxin groups
Toxin groupChemistry and actionMain effectsExamples of producing genera (some strains)
MicrocystinsCyclic peptides (many variants, e.g., microcystin-LR) that inhibit protein phosphatasesLiver damage (hepatotoxins); the most frequently detected groupMicrocystis, Planktothrix, Dolichospermum, some benthic genera
AnatoxinsAlkaloids (anatoxin-a, homoanatoxin-a) that act on nerve–muscle signalingRapid neurotoxic effects: tremors, paralysis, respiratory failureDolichospermum, Aphanizomenon, benthic Microcoleus
CylindrospermopsinsAlkaloid that inhibits protein synthesisLiver, kidney and other organ damage (cytotoxin)Raphidiopsis, some Aphanizomenon-related genera
SaxitoxinsAlkaloids that block nerve sodium channelsParalytic effects (the same toxins as paralytic shellfish poisoning)Aphanizomenon, Dolichospermum, Raphidiopsis, benthic genera

Benthic cyanobacteria are not a separate, safer category: mats in rivers and lakes produce most of the same toxins, including microcystins, anatoxins, cylindrospermopsins and saxitoxins, and they have been involved in many animal poisonings [14, 15]. Other cyanobacterial compounds — skin irritants and lipopolysaccharides from the cell envelope, for example — can cause rashes and other symptoms after recreational contact [14, 16].

Toxin mixtures are common. In blooms sampled from 23 Midwestern lakes, microcystins occurred in every bloom, and many blooms contained several toxin groups along with taste-and-odor compounds [6]. Nationally, the 2007 EPA National Lakes Assessment detected microcystins in 32% of samples, saxitoxins in 7.7% and cylindrospermopsins in 4.0% [17].

5.5Intracellular versus dissolved toxin

Most microcystin in an actively growing bloom is held inside living cells (intracellular). It is released into the water (dissolved or extracellular) when cells age, die or are broken — by natural decline, by grazing, or by treatments such as algaecides that rupture cells. Cylindrospermopsin, in contrast, is often found largely dissolved [13, 16]. This distinction has practical consequences:

  • Sampling. A "total" toxin analysis requires lysing cells (for example, by repeated freeze–thaw) before measurement; filtering the sample first measures only the dissolved fraction. Results must say which was measured.
  • Treatment. Conventional drinking-water treatment can remove intact cells and low levels of toxins, but severe blooms require planning, because treatments that break cells can move toxin into the dissolved phase, where it is harder to remove [18].
  • Timing. Dissolved toxin can persist after a visible bloom has disappeared, so "the water looks clear now" is not evidence that it is safe [13].

5.6Oxygen depletion

A dense bloom swings dissolved oxygen through a daily cycle: photosynthesis can supersaturate surface water in the afternoon, while respiration by the same cells and by bacteria can drive oxygen very low before dawn. When the bloom collapses, decomposition of the dead biomass consumes oxygen further, especially in warm, stratified water where the bottom layer is cut off from the atmosphere. The result can be fish kills and the release of phosphorus from oxygen-poor sediments, which feeds the next bloom [3, 19]. For field researchers, this means a single daytime oxygen reading can badly misrepresent conditions; time of day must be recorded with every measurement.

5.7Cells, color and toxins are not interchangeable

Several different numbers are used to describe blooms, and each answers a different question [13, 17]:

Table 5.2. What common bloom measurements can and cannot tell you
MeasurementTypical unitsWhat it indicatesWhat it cannot tell you
Visual appearance, color, scumDescriptive; photographsThat a bloom may be present; prompts samplingWhich organisms, how many, or whether toxins are present; look-alikes are common
Cell counts or biovolumecells/mL; mm³/LAbundance of cyanobacteria (by genus, if identified)Toxin concentration; toxic and non-toxic strains are counted alike
Chlorophyll aµg/LTotal phytoplankton biomassWhether the biomass is cyanobacteria at all
Phycocyaninµg/L or relative fluorescence unitsRelative cyanobacterial biomassSpecies, toxin genes or toxins
Toxin genes (qPCR)gene copies/mLPresence and abundance of potential toxin producersWhether toxin is actually being produced, or how much
Toxin concentration (ELISA, LC-MS/MS)µg/L (= parts per billion)Exposure-relevant toxin levels; compared with health guidanceWhich organism produced it; ELISA reports a toxin class, not each variant

The evidence that these differ is direct. In Northern Kentucky urban ponds monitored for a year, microcystin levels did not always coincide with high Microcystis cell counts [20]. In the national lakes survey, cyanobacteria were present in 98% of samples but microcystins were detected in about a third [17].

Kentucky's practice has changed over time

Kentucky Energy and Environment Cabinet news releases show the state moving from cell counts to toxin concentrations. In 2013 the Division of Water planned to issue "advisories" above 20,000 cells/mL and "cautions" above 100,000 cells/mL [21], and in 2014 it lifted cautions when counts fell below 100,000 cells/mL [22]. By 2015, releases described a recreational threshold of 20 parts per billion of microcystins [23], and in 2016 a two-tier system of a public health watch ("toxins are present at levels that may affect sensitive populations") and a warning ("toxins present are at unsafe levels") [24, 25].

Current thresholds: recent releases say only "advisory threshold," and the EPA's 2026 table of state thresholds lists none for Kentucky, noting that it includes only publicly accessible values [26]. Confirm current practice on the Division of Water HAB page (opens in a new tab).

5.8Effects on fish, livestock, pets, wildlife and people

Animals are often the first victims. Dogs are especially vulnerable because they swim in, drink and lick bloom material and mats from their fur; U.S. records of suspected and confirmed canine cyanotoxin poisonings span nearly a century [27]. Livestock drinking from enriched farm ponds are also at risk — and two of the very few published Kentucky records are livestock cases: pigs poisoned by a pond bloom attributed to Anabaena (now Dolichospermum) in 1989, and 15 cattle that died around two ponds in August 2013, with microcystin-LR detected in one pond and in rumen contents [28, 29]. Because animal illnesses often precede or accompany human exposures, they can serve as sentinel events for public health [30].

Fish are affected mainly through oxygen depletion during bloom decline, and also by toxins [3].

People are exposed by swallowing water while swimming, by skin contact, by inhaling spray during activities such as water-skiing, and through drinking water [12, 31]. Symptoms range from skin rashes, eye irritation and gastrointestinal illness to, at high doses, liver or nervous-system effects. Young children are of particular concern, which is why EPA's drinking-water advisories set lower values for bottle-fed infants and pre-school children (Table 5.3) [32].

5.9Recreational and drinking-water guidance

Guidance values are concentrations at or below which health effects are not expected for a given exposure. They are not legally enforceable unless a state adopts them. For U.S. waters, the EPA has issued:

Table 5.3. U.S. EPA guidance values for two cyanotoxins (µg/L)
ToxinRecreational criterion / swimming advisory (2019)Drinking water, 10-day health advisory: bottle-fed infants and pre-school children (2015)Drinking water, 10-day health advisory: school-age children and adults (2015)
Microcystins80.31.6
Cylindrospermopsin150.73.0

Sources: EPA recreational recommendations [33] and drinking-water health advisories [32]. The much lower drinking-water values reflect daily ingestion over many days, compared with occasional swallowing during recreation. Note that 1 µg/L equals 1 part per billion (ppb).

5.10Monitoring and advisories in Kentucky

In Kentucky, the Division of Water and the Department for Public Health issue harmful algal bloom recreational advisories jointly [34]. The state's bloom record in Cabinet releases begins in 2013, when the U.S. Army Corps of Engineers identified a bloom on Taylorsville Lake and then found elevated cyanobacteria in several Corps lakes, prompting the Division of Water to begin testing 14 other lakes [35, 21]. The largest events were on the Ohio River: in September 2015, advisories eventually extended from the West Virginia line downstream to the Cannelton Locks and Dam [36], and in 2019 an advisory covered the river from McAlpine Dam to Greenup Dam [34]. EPA-led modeling has since linked bloom occurrence and persistence on the river to antecedent flow conditions, calibrated on the 2015 and 2019 events [37], and USGS sampling has shown that cyanotoxins occur in large rivers even without visible blooms [38]. Chapter 9 reviews the Kentucky record in more detail.

For current conditions, use the official sources in the Resource Library: the Division of Water's HAB page and Water Maps Portal (which includes a HAB viewer), and the Department of Fish and Wildlife Resources guidance for anglers and boaters.

5.11Safety rules for student researchers

Field and laboratory rules
  • Check advisories before every visit; do not sample where an advisory is in effect unless it is part of an approved, supervised protocol.
  • Wear gloves when handling water, sediment or biofilm; avoid splashing and spray; wash hands before eating.
  • Never touch, wade through, or collect surface scums or detached mats; photograph them from the shore and report them to faculty.
  • Do not culture, concentrate, aerosolize, or freeze–thaw suspected toxic material in the teaching laboratory. Toxin analysis is done by qualified laboratories [39].
  • Keep dogs away from all field sites.

5.12Connection to local research

At Allen Branch

There are no observations of blooms, mats or toxins in Allen Branch, and this portal does not describe it as a bloom site. Hypothesis If cyanobacteria occur there, benthic mats are the form most likely to matter, as in other wadeable streams [40, 41].

A responsible first step is descriptive: document biofilm types, photograph them, and record water temperature, flow and canopy at defined stations. If mats with a cyanobacterial appearance are found, faculty decide whether to send samples to a qualified laboratory for toxin analysis. See the field safety page.

Key terms

Bloom
Rapid increase in algal or cyanobacterial biomass.
Harmful algal bloom
A bloom that causes harm through toxins, oxygen loss, taste and odor or habitat change.
Cyanotoxin
Toxic compound produced by some cyanobacterial strains.
Microcystins
Cyclic-peptide liver toxins; the most commonly measured cyanotoxins.
Intracellular toxin
Toxin held inside living cells.
Dissolved toxin
Toxin free in the water after cells release it.
Health advisory
Non-regulatory guidance concentration for a given exposure period.
µg/L (ppb)
Micrograms per liter; parts per billion.

Knowledge check

  1. Two ponds have the same Microcystis cell count. Pond A has 12 µg/L microcystins; Pond B has none detected. Give two biologically plausible explanations.

    Show answer and explanation

    The ponds may contain different proportions of toxin-producing genotypes; or the populations may differ in how much toxin they are producing under current conditions. (Analytical differences — total versus dissolved toxin — should also be checked.)

  2. A bloom was treated with an algaecide yesterday and the water looks clearer today. Why might toxin concentrations in the water be higher?

    Show answer and explanation

    Algaecides rupture cells, releasing intracellular toxin into the water as dissolved toxin, which can persist after the cells are gone.

  3. A lake sample has 5 µg/L microcystins. How does that compare with the EPA recreational value and the 10-day drinking-water advisory for adults?

    Show answer and explanation

    It is below the 8 µg/L recreational value but above the 1.6 µg/L 10-day drinking-water advisory for school-age children and adults — water that may be acceptable for swimming is not acceptable to drink untreated.

  4. Why should every dissolved-oxygen reading taken near a bloom include the time of day?

    Show answer and explanation

    Oxygen rises during daylight photosynthesis and falls at night through respiration, so the same site can range from supersaturated in the afternoon to very low before dawn.

  5. Kentucky releases from 2013 describe cell-count thresholds; releases from 2015 describe a microcystin threshold. Why might an agency make that change?

    Show answer and explanation

    Health risk depends on toxin exposure, and cell counts do not reliably predict toxin concentrations; toxin measurements relate directly to health-based guidance values.

References

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  2. U.S. Environmental Protection Agency (n.d.). Visually Identifying Signs of a Cyanobacterial Bloom. U.S. EPA Harmful Algal Blooms program. https://www.epa.gov/habs/visually-identifying-signs-cyanobacterial-bloom (external site, opens in a new tab) (accessed 2026-11-05)
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  32. U.S. Environmental Protection Agency (2015). EPA Drinking Water Health Advisories for Cyanotoxins. U.S. EPA Harmful Algal Blooms program. https://www.epa.gov/habs/epa-drinking-water-health-advisories-cyanotoxins (external site, opens in a new tab) (accessed 2026-11-05) 10-day health advisories (2015): microcystins 0.3 µg/L (bottle-fed infants and pre-school children) and 1.6 µg/L (school-age children and adults); cylindrospermopsin 0.7 and 3.0 µg/L.
  33. U.S. Environmental Protection Agency (2019). Protecting Human Health from Cyanotoxin Exposure During Recreation. U.S. EPA Harmful Algal Blooms program. https://www.epa.gov/habs/protecting-human-health-cyanotoxin-exposure-during-recreation (external site, opens in a new tab) (accessed 2026-11-05) States EPA's 2019 recommended recreational criteria/swimming advisory values: microcystins 8 µg/L, cylindrospermopsin 15 µg/L.
  34. Kentucky Energy and Environment Cabinet (2019). Harmful Algal Bloom Recreational Public Health Advisory Issued. Naturally Connected (Cabinet news). https://kydep.wordpress.com/2019/09/26/harmful-algal-bloom-recreational-public-health-advisory-issued/ (external site, opens in a new tab) (accessed 2026-11-05)
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  36. Kentucky Energy and Environment Cabinet (2015). Recreational advisory issued for Ohio River due to harmful algal bloom. Naturally Connected (Cabinet news). https://kydep.wordpress.com/2015/09/18/recreational-advisory-issued-for-ohio-river-due-to-armful-algal-bloom/ (external site, opens in a new tab) (accessed 2026-11-05)
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