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Harmful Algal Blooms: Safety, Testing, and Management Options

This article discusses what harmful algal blooms (HABs) are and summarizes quick identification tips, water testing, and bloom control methods.

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Updated:

July 15, 2025

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Harmful Algal Bloom (HAB) in Lake Erie waters. Photo Credit: Anna McCartney, Pennsylvania Sea Grant.

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What are Harmful Algal Blooms?

Cyanobacteria are microscopic organisms that occur naturally in surface water sources. They are also called blue-green algae; however, cyanobacteria are merely bacteria that can photosynthesize. Cyanobacteria support aquatic ecosystems when present at low levels in ponds, lakes, and rivers. However, under the right conditions, including the presence of excessive nutrients like phosphorus and nitrogen in the water, warm temperatures, sunlight, and calm water, cyanobacteria can form large blooms in surface water.

Harmful algal blooms, or HABs, occur when colonies of cyanobacteria grow out of control. They are considered HABs for a variety of reasons:

Some cyanobacteria species can produce harmful toxins called cyanotoxins and odorous byproducts known as taste and odor (T&O) compounds. Cyanotoxins can sicken and kill animals, including birds, pets, livestock, etc., and can also have adverse effects on human health. T&O do not have an impact on health, but can cause water to have an earthy and musty smell or taste.
In addition to the toxic and odorous by-products, cyanobacteria blooms can discolor water, causing a bluish green, brown, whitish, or reddish color on the surface of ponds, lakes, and rivers. They can also form thick scums or floating mats on the water surface.
Finally, as cyanobacteria cells from large blooms decay, they deplete oxygen in the water column and clog the gills of fish and invertebrates, potentially resulting in large fish kills.

How is Nutrient Pollution Connected to Harmful Algal Blooms?

Nutrients like nitrogen and phosphorus occur in natural cycles in all aquatic habitats. When present in excessive amounts, nutrient availability is shifted out of balance. This can cause cyanobacteria and other aquatic plants to thrive and use excessive nutrients to grow rapidly.

How do Nutrients Enter Waterbodies?

Natural nutrient cycles: Erosion and the water cycle contribute nutrients naturally into a water body. When naturally occurring in balance, nitrogen and phosphorus are critical for aquatic plant life.
Human and animal waste inputs: Nutrients are present in human and animal waste. If not properly treated or bound by strict treatment guidelines, nitrogen and phosphorus can be released into natural waterways through the discharge of wastewater effluent after treatment. Poorly maintained septic systems can also contribute human waste and additional nutrients to surrounding waterbodies.
Runoff from urban and farming areas during heavy rain: Urban lawn care and agricultural practices can contribute excessive nutrients to waterways. Nutrients from fertilizer, manure, and biosolids applied improperly can migrate from lawns and farm fields either into stormwater drains or directly into a nearby stream or pond during heavy rains.
Legacy nutrients: Phosphorus naturally binds to underwater sediment as phosphate. If the water body develops a zero oxygen zone, or anoxic zone, the chemical reaction causes phosphate to be released from the sediment and into the water column.

Is it Cyanobacteria or Green Algae?

Cyanobacteria and green algae are both common in water bodies and can form blooms. This table provides some characteristics that distinguish between good algae (green algae) and harmful algal blooms (cyanobacteria):

Table 1: Differences between blooms from cyanobacteria and green algae
Characteristics	Cyanobacteria	Green algae
Bloom appearance	Some cyanobacteria species can cause blooms that look like paint, pea soup, or thick floating scums or mats	Stringy and slimy floating mats
Bloom color	Some cyanobacteria species can cause blooms that are bluish-green, red, brown, or whitish	Typically bright green
Stick or paddle test: Safely dip a sturdy stick/paddle in lake/pond to assess surface mats	The stick or paddle may look like it was dipped in paint	Filamentous green algae are likely to attach to the stick or paddle
Floating jar test: While wearing gloves, collect and fill a clear jar halfway with a sample from a lake/pond and allow it to sit undisturbed for 15-130 minutes.	Cyanobacteria will float to the top of the jar	Green algae will settle to the bottom of the jar
Smell test	Some species produce by-products that can make water have an earthy or musty smell	Do not produce odorous byproducts, but may have a swampy odor
Toxin production	Some species of cyanobacteria produce harmful toxins. Toxins can only be confirmed through a water test	Do not produce toxins
Drinking water and recreational risks	High risk if the bloom species is toxin-producing. Toxins can be harmful to pets, livestock, birds, and humans	Low risk, however mats may be unpleasant and a nuisance

Although the visual inspection tips can help with initial differentiation between cyanobacteria and green algae, water quality testing may be needed to: (i) assess bloom activity or stress conditions, (ii) confirm the presence of cyanobacteria, (iii) accurately identify cyanobacteria species and enumerate cell concentrations, and (iv) confirm toxin or T&O compounds production. The type of testing chosen should align with the intended goals or desired understanding from the test results. Table 2 below summarizes some common water quality tests and how to interpret them.

Table 2: Water quality testing for HABs and how to interpret results
Test type	Testing capabilities	What do the test results say?	How to interpret results
Secchi depth for turbidity	Field testing using a Secchi disk and laboratory testing of turbidity	Water clarity or cloudiness due to bloom biomass or sediments	Transparency <3 m may indicate low water clarity from blooms
Nutrients	Nitrogen test strips are available for field use. Laboratory testing is needed for accurate nutrient levels	Concentration of nitrogen and phosphorus in water	Total phosphorus (TP) >0.035 mg/L and nitrate > 3mg/L show eutrophic conditions that can promote cyanobacteria, green algae and other aquatic plant growth
Dissolved oxygen (DO)	Handheld meters and kits are available for field testing	Indirect signs of bloom-induced stress	DO <2-3 mg/L shows hypoxia or low levels that can harm or kill aquatic life
Chlorophyll-a (green photosynthetic pigment produced by cyanobacteria and green algae)	Possible field testing using calibrated meters. Laboratory testing available	An indicator of total cyanobacteria and algae biomass	Chlorophyll-a >10 µg/L shows increased productivity and likely presence of cyanobacteria or green algae
Phycocyanin (blue photosynthetic pigment produced only by cyanobacteria)	Possible field testing using calibrated meters. Laboratory testing available	An indicator of total cyanobacteria biomass	Detection of phycocyanin shows that cyanobacteria are present. Higher concentrations correspond with high levels of cyanobacteria
Microscopy	Laboratory analysis needed	Identification of the type of cyanobacteria or green algae species present. Enumeration (cells/mL) of cyanobacteria or algal cell concentrations	Species like Microcystis sp., Cylindrospermopsis sp. Can produce toxins. <20,000 cells/mL: potential irritative or allergen impacts 20,000 – 100,000 cells/mL: potential adverse effects from toxin production >100,000 cells/mL: High risk from skin contact with water
Toxin testing	Field testing ELISA kits available. Laboratory testing available	The presence or absence of cyanotoxins	US EPA swimming advisory: Not safe for swimming if microcystin >8 µg/L and cylindrospermopsin is >15 µg/L

The US EPA maintains a nationwide database of laboratories that can conduct analysis for cyanobacteria and cyanotoxins. To find a testing laboratory, search Laboratories that Analyze for Cyanobacteria and Cyanotoxins. Penn State Extension Agricultural Analytical Service Laboratories provides a pond and lake testing package that includes nutrients.

How Can Cyanobacterial Blooms be Controlled?

The most proactive method to control cyanobacterial blooms is to prevent or control nutrient pollution. Once a bloom is established, there are different chemical, mechanical, and biological methods that can be implemented to manage cyanobacteria. There is no silver bullet when it comes to bloom control. Each method has a different mode of action, which is the mechanism through which a bloom is controlled, advantages and disadvantages.

Table 3: Summary of bloom control methods
Control method	Mode of action	Strengths	Weaknesses
Nutrient-removing chemicals, e.g., aluminum sulfate, lanthanum bentonite,	Chemicals that react and bind excess phosphorus are added in the water column	- Internal nutrient removal - Long-term treatment effect	- Ineffective if external nutrient pollution sources are not controlled - Treatment influenced by water chemistry e.g., pH, alkalinity, organic matter content - Permit may be required in some regions
Peroxide-based algaecides	Hydrogen peroxide is a strong oxidant. When used to control cyanobacteria, it damages cell structure and function, thereby resulting in cell death	- Rapid water quality improvements - Minimal ecological impact if dosed correctly - Selective to cyanobacteria - Inexpensive	- Permit required - Short-term control method as bloom can rebound - Release of cyanotoxins due to cell death - Peroxides have short residence times in water - Does not remove nutrients in the water column - Ineffective if external nutrient pollution is not controlled
Copper-based algaecides	Copper ions are toxic to cyanobacteria cells. Copper limits photosynthesis, hence resulting in cell death.	- Rapid water quality improvements - Inexpensive - Long residence time	- Permit required - Short-term control method as bloom can rebound - Release of cyanotoxins due to cell death - Does not remove nutrients in the water column - Copper accumulation in sediments and water column - Impact on non-target species - Ineffective if external nutrient pollution is not controlled
Ultrasonication	Ultrasonic irradiation in water disrupts the cyanobacteria cells' ability to float. Cells settle to the bottom, thus have reduced ability to photosynthesize and cells die off	- No chemical addition or residuals - Potential selectivity to cyanobacteria	- Potential toxin release - Treatment efficacy is impacted by source water size and geometry - Limited field-scale application trials and success - May impact aquatic organisms - Ineffective if external nutrient pollution is not controlled
Artificial mixing	Mechanical mixing of water to limit stratification of the water column and increase dissolved oxygen levels in the sediment zone. Oxygenated conditions reduce the release of nutrients bound in sediments.	- Increases dissolved oxygen in water - Can suppress the release of nutrients in the sediment zone - Long-term treatment benefits if sized correctly and used continuously	- Costly installation and operation - Suspension of sediments and nutrients in the water column - Ineffective in shallow water bodies - Ineffective if external nutrient pollution is not controlled
Hypolimnetic oxygenation	Hypolimnion is the deepest part of a stratified lake or pond. Oxygenation in this zone increases dissolved oxygen levels without disrupting thermal stratification. Oxygenated conditions reduce the release of nutrients bound in sediments	- Increases dissolved oxygen in bottom layers - Can suppress the release of nutrients in the sediment zone - Avoids the potential mixing of nutrients from sediments in the water column - Long-term treatment benefits if sized correctly	- Costly installation and operation - Suspension of sediments and nutrients in the water column - Ineffective if not sized correctly or optimized based on water body size and geometry - Ineffective if external nutrient pollution is not controlled
Sediment dredging	Involves excavating sediments in a lake or pond and relocating them to a disposal site. By removing nutrient-rich sediments, this method controls internal loading of nutrients	- Removes nutrient-rich sediments - Increase dissolved oxygen levels	- Costly - Permit required - Disposal needs for dredged materials - Potential suspension of sediments and nutrients - Ineffective if external nutrient pollution is not controlled
Biological methods, e.g., the use of barley straws or fish addition	As barley straws decay, they release chemicals that limit cyanobacteria growth. Reducing planktivorous fish to increase populations of grazers that can feed on algae and cyanobacteria	- Long-term treatment benefits if treatment is optimized and sized correctly - No chemical addition and residuals - Minimal ecological impacts	- Treatment effect is localized - Barley straws do not control nutrients - Straws may be ineffective in low dissolved oxygen levels - Fish addition or removal may result in population shifts - Permits for fish stocking are required in some regions - Ineffective if external nutrient pollution is not controlled

How can You Prevent Harmful Algal Blooms?

Preventing large blooms of cyanobacteria can be accomplished in small waterbodies by managing excessive nutrients. Use these tips to reduce Harmful Algal Blooms in your area!

Always apply fertilizer according to the 4Rs: right source, right rate, right time, right place
Have septic systems inspected and serviced regularly
Limit/prevent livestock from accessing ponds
Control nuisance wildlife populations e.g., Canada geese on pond
Establish vegetative buffers around pond/lake.
Pick up pet waste
Implement runoff management techniques like rain barrels and rain gardens to slow and sink runoff
Get your property certified through the Watershed Friendly Property Program

How to Stay Safe while Recreating

HABs are a natural occurrence, but they can pose serious health risks to humans and animals alike. These blooms can produce harmful toxins and are most prevalent in warmer months. Be sure to stay vigilant and safe when recreating in and around the water during the summer months.

When harmful algal blooms occur, the water may appear discolored, often resembling thick green or blue-green mats. Toxins that are harmful if ingested, inhaled, or come into contact with the skin can be produced by the algae, and may be present even when visible scums and mats have dissipated.

Safety First

Harmful effects: Exposure to toxin-producing cyanobacteria can cause skin rashes, respiratory issues, gastrointestinal distress, and more severe symptoms if ingested or inhaled.
High-risk areas: Visitors should exercise caution near still waters, such as ponds or slow-moving streams, where these blooms are most likely to occur.
Do not use ponds for swimming, boating, fishing, or watering animals when there is a suspected cyanobacteria bloom.

What You Can Do

Be Safe in or near the Water if you observe any indicators that HABs are present
- Stay Informed! To coordinate monitoring, response, and communications about HABs in Pennsylvania, several Commonwealth agencies and commissions formed the Pennsylvania HABs Task Force. They publish the Harmful Algal Bloom Dashboard, where they provide field and laboratory monitoring data and post advisories. You can also call park managers and your local health department ahead of recreating.
- Follow all posted warnings and advisories, even if the water looks clear: Postings advising users to "Avoid Contact" mean that cyanobacteria cells and/or the toxins have been detected at levels that can be harmful to pets and humans. Avoid swimming, wading, boating, or fishing in areas with posted advisories.
- Avoid areas with visible blooms: Even without posted warning signs, it is prudent to keep pets and children away from and avoid swimming, wading, or fishing in areas with visible algae blooms.
- Rinse off with fresh water immediately after swimming, even in areas not affected by blooms.

By staying informed, avoiding areas with visible algae, and practicing common-sense safety measures, you can avoid the risks associated with harmful algal blooms. When in doubt, stay out!