Harmful Algal Blooms - HABs

What is a Harmful Algal Bloom?

Algae are fundamental to life on earth as the foundation of aquatic ecosystems and the originators of the production of oxygen via photosynthesis. Even today algae produce 50% of the oxygen in the earth's atmosphere, as summarized in this excellent overview from 2010 by Chapman.

The term harmful algal bloom (HAB) came about due to minor players in the world of photosynthetic organisms, especially the toxic blue green algae in freshwater lakes, reservoirs, rivers and streams, and toxic diatoms and dinoflagellates like the Florida red tide dinoglagellate Karenia brevis in coastal environments.

algae types microalgae species
1Source: U.S. National Office of Harmful Algal Blooms, WHOI

"Harmful algal bloom" describes overgrowth of these problem species, considered harmful mainly because of their ability to product toxins. The toxic cyanobacteria include the commonly tracked genera of Microcystis, Dolichospermum (formerly Anabaena) and Cylindrospermopsis that threaten drinking water sources globally, and which produce a variety of hepatotoxins (liver toxins) and neurotoxins. The toxins produced by this wide range of algal species can be harmful to animals and humans alike, with consequences ranging from itchy skin or headaches to chronic impacts like liver disease and in very rare cases, even death.

algae toxins

Learn more about HABs from experts:

What Causes Harmful Algal Blooms?

As mentioned above toxic blue green algae are photosynthetic: they use carbon dioxide, water and sunlight to incorporate carbon and hydrogen into the building blocks for their cells. Carbon and hydrogen (in the form of glucose) are not enough for growth: nitrogen, phosphorus, sulfur, vitamins and other micronutrients are obtained from the environment, and different species have different requirements for temperature, salinity, and other water conditions to thrive.

algae photosynthesis

In a healthy water body nitrogen and phosphorus are cycled through both the biological and non-biological components of the system, and bilogically assimilable forms (especially nitrate and orthophosphate) are at low enough concentrations to keep algal growth in check. But nutrient enrichment, called eutrophication, can enable blue green algae to outgrow other types of algae. This is in part because cyanobacteria, being bacteria, grow faster even in the best of conditions for other algae.

Historically phosphorus was considered more important than nitrogen for stimulating HABs, certainly in freshwater systems. But in the early 2010s leading researchers such as Paerl and Scott (2010) and Davidson et al. (2012) started to demonstrate that an overabundance of both nitrogen and phosphorus must be considered as important causes of HABs.

Source: Alliance for the Great Lakes

Learn more about causes of HABs:

The Impacts of HABs

The harmful outcomes of HABs are not limited to toxins. Three common areas of concern are:

  1. The quality and safety of drinking water,
  2. Protection of wildlife, livestock and other animals (including humans!), and
  3. Local economies.

An event that crystallized the public's awareness of the threats HABs pose to drinking water occurred in 2014 in YSI's home state of Ohio, when Lake Erie was overwhelmed by an HAB that generated high levels of microcystin toxin, which the Ohio EPA detected in the City of Toledo's finished drinking water. The ensuing "Do not Drink" advisory left nearly half a million people without potable water and made national and global headlines. The National Guard distributed bottled water, but in the end hundreds of water-intensives Toledo-area businesses lost income and the total economic impact has been estimated at $65 million, according to this brochure by NOAA's Great Lakes Environmental Research Laboratory.

Perhaps the most frequent example of HABs affecting wildlife are the massive fish kills they can induce. Fish kills occur for two reasons. The first is that the HABs can induce hypoxia, a depletion of dissolved oxygen that can essentially suffocate fish. There are also toxins produced by algae, particularly in marine environments, that kill fish and other animals. For example, a massive red tide in 2018 may be to blame for bottlenose dolphin deaths studied by NOAA. Inland, livestock and migratory birds are also affected by HABs. In fact livestock deaths were the reason for some of the earliest discoveries of potent algal neurotoxins.

And yes, sadly, beloved family pets are also vulnerable to the effects of HABs. This brochure by New York's NOAA Sea Grant program has information about dogs and HAB poisonings.

harmful algal blooms toxins

Finally the commercial and political repercussions of HABs are also significant, though they have been hard to trakc comprehensively. At the height of Florida's 2018 red tide, 40 Pinellas County businesses claimed $128 million in lost revenue. Outgoing Florida Governor Rick Scott made millions of grant dollars available for cleanup of dead fish, and within days of taking office in January 2019 Governor Ron DeSantis' Executive Order created an Office of Environmental Accountability and Transparency within the Department of Environmental Protection. Businesses that rely upon tourism are heavily impacted when beaches and shorelines close due to HABs.

Learn more about HAB impacts to drinking water, animals, and economies:

These causes and consequences of HABs are all linked to water quality, and water quality monitoring can aid in the prevention, early detection, and management of HABs.

Water Quality and Harmful Algal Blooms

The key to successful HAB management is early detection, which requires diligent monitoring. People monitor HABs in a number of ways:

  • Algae species are identified via microscopy, DNA-based methods, and flow-based imaging technologies,
  • Toxins are detected via enzyme-linked immunosorbent assays, HPLC, and via molecular biology methods,
  • Satellites can be used to visualize system-wide presence of potentially toxic algae, such as the Harmful Algal Blooms Monitoring System from NOAA.

All of these approaches have inherent advantages and disadvantages related to speed, costs, reliability, and the level of expertise required to use each tool. Each approach is greatly aided by incorporating water quality monitoring for both the early detection of HABs as well as for understanding bloom dynamics and impacts.

The water quality parameters below are listed in their order of importance for HAB Monitoring are:

algal pigments

Algal Pigments. Algae have unique pigments that they are use for photosynthesis, and for HAB monitoring chlorophyll, phycocyanin and phycoerythrin are very useful. Chlorophyll has been used for decades to monitor the growth of any type of algae. The pigment phycocyanin is a more specific indicator of blue-green algae in freshwater systems, and a similar pigment called phycoerythrin is a useful indicator of blue-green algae in marine systems.


Nitrate. YSI's HAB monitoring enthusiasts, like everyone else, eagerly awaited the launch of the EXO NitraLED sensor because of the high relevance of nutrient pollution for stimulating HABs. Nitrate is one of two key nutrients, the other being phosphorus, that typically are limiting for algal growth in a healthy water body. The addition of NitraLED to a monitoring program is important for understanding eutrophication in a freshwater system. In saltwater systems looking for fluorescent dissolved organic matter (fDOM) might be helpful, too.

Dissolved oxygen

Dissolved Oxygen (DO). Oxygen is a product of photosynthesis, and in a balanced diurnal cycle of photosynthesis and respiration, algae generate adn consume oxygen, respectively. Meanwhile other organisms consume oxygen around the clock. During the early and peak growth phases of an HAB, DO can increase significantly due to high photosynthetic activity during the day. As the bloom fades and dies, the algae become food for bacteria and other things that consume oxygen, and DO levels can drop precipitously. Learn more about DO sensors in our DO Handbook.

pH in water

pH. Like DO, pH responds to the growth of algae, typically increasing with increased algal growth. As with DO, this is in part due to the balance between photosynthesis, which in this case consumes dissolved carbon dioxide, and respiration, with generates carbon dioxide. One of the main forms of carbon dioxide dissolved in water is carbonic acid (H2CO3), which as the name suggests, has a low pH. It is in equilibriumwith other carbon forms, notably bicarbonate (HCO3-) and carbonate (CO3-). As algae consume CO2, less of the gas dissolves into the water as carbonic acid, and pH will increase, eventually reaching 9 or 10 during severe HABs.

temperature in water

Temperature. Warming waters, due to climate change, the changing of seasons, or thermal pollution, favor the proliferation of most blue-green algae that form HABs in freshwater systems. In coastal systems, many red and brown-tide forming algae also have a preference for specific temperature ranges. While it affects the growth of the algae, temperature isnt affected by algae, distinuguishing it from pigments, DO, and pH parameters discussed above. Thus the utility of monitoring temperature as part of a HAB program is to have a better understanding of when temperatures reach the optima for the algae that most often bloom in a system.

photosynthetically active radiation

Photosynthetically Active Radiation (PAR). PAR is the amount of sunlight that diffuses through water compared to surface light, thus affecting the availability of light for algae to grow. Understanding PAR and how it changes daily, seasonally, or with treatment strategies will aid in the management of HABs, especially when combined with the parameters above.


Turbidity. Turbidity can interfere with light emitted by a sensor, and thus can be an interference in algae monitoring. Turbidity can detect a plume of sediment from a runoff event-sometimes an indicator of nutrient introduction, and measurement of turbidity is a requirement for use of the NitraLED sensor.


fDOM. Flourescent dissolved organic matter (fDOM) is a fraction of organic matter in the water. The same conditions that can lead to high organic matter in water, in some environments, can foster algal growth. Note also that high organic matter can sometimes interfere slightly with measurements of chlorophyll.

YSI's HAB Monitoring Tools: From Sensors to Systems

YSI provides the most advanced water quality monitoring platforms in the world, especially the continuous-monitoring EXO platform and the spot-monitoring ProDSS platform. Both platforms support a suite of sensors for other water quality parameters like those listed above.

YSI's unique dual-channel pigment sensors, called total algae (TAL) sensors, were first introduced for EXO. The EXO TAL-PC sensor can detect both chlorophyll and phycocyanin, and the EXO TAL-PE sensor can detect both chlorophyll and phycoerythrin. Due to high demand for these same sensors in a more mobile sampling context, in 2018 we added the ProDSS TAL-PC and ProDSS TAL-PE sensors.

As a general rule, the TAL-PC sensors are for freshwater monitoring, and the TAL-PE sensors are for saltwater. However that is not an abosulte rule, and in this blog about the Top 5 HAB Monitoring Questions, Dr. Stephanie Smith explains why.

These sensors are a significant tool for early detection because they are placed right in the water-there is no sample collection, no extraction, and no lab processing to obtain readings in real time.

Once either the TAL-PC or TAL-PE sensor is selected, the combinations of sensors, sondes and systems are almost endless. to make it easier to get started, YSI has designed HAB Monitoring Sonde Packages shown below. Similar packages can be adapted for the ProDSS platform, though it should be noted that the ProDSS cannot support NitraLED or fDOM.

Peope incorporate these sonde packages into standalone monitoring stations and into buoys with data telemetry into HydroSphere, so they have 24/7 visibility of water quality. In HydroSphere they can even set alerts and notifications when specific parameter reach thresholds that are suggestive of conditions favoring harmful algal blooms. The Photosynthesis sonde packages can also be incorporated into vertical profiling systems and most recently, remote or autonomous vehicles. The Eutrophication Sonde packages are being tested in these systems, since the NitraLED sensor is still very new.

One example of a complete solution that can be deployed very rapidly for HAB monitoring is YSI's DB600 HAB Monitoring solution. This system can be put together and deployed by one person, and pre-configured systems make them easy to select.

Below the description of the HAB Monitoring Sonde Packages, there is a link to a guided questionnaire that will help a YSI associate point you directly to the right HAB monitoring solution for your needs.

HAB Sonde Packages

YSI makes HAB monitoring easy by offering pre-configured EXO sonde packages that combine the most relevant suite of sensors for detecting algae and relevant water quality parameters. Have a ProDSS or a 4-port sonde--no problem! These packages can be adapted to any YSI platform.

Photosynthesis Package

Harmful Alagal Bloom monitoring system

The Photosynthesis Package will detect the early signs of photosynthetic activity and algal growth, positioning you for a rapid response with the following sensors:

  • TAL-PC (freshwater) or PE (saltwater)
  • DO
  • pH/ORP
  • Wiped C/T
  • Central Wiper

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Eutrophication Package

Harmful Alagal Bloom monitoring system

The Eutrophication Package will detect the early signs of photosynthetic activity and algal growth, positioning you for a rapid response with the following sensors:

  • TAL-PC (freshwater) or PE (saltwater)
  • DO
  • pH/ORP
  • Turbidity
  • NitraLED (freshwater) or fDOM (saltwater)

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EXO PAR Package

Algae monitoring system

YSI's Integrated Systems team has designed a unique bracket system and adapter for the Auxiliary port of the EXO2 sonde. Add PAR to the Phototsynthesis or Eutrophication sensor suites above and get yoru data in the EXO handhelds, KOR software, or HydroSphere! Learn more here.

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HAB Blog Posts

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