Seymour Lake

Anyone who enjoys being on the water should become familiar with cyanobacteria. These photosynthetic native organisms are found in many Vermont lakes and ponds. They can float in the water, grow attached to plants and rocks, or grow directly on the bottom. Some cyanobacteria produce potent toxins that are harmful to people, pets, and other animals. Under certain conditions, cyanobacteria can grow so thickly that they color the water green, blue, or white. These events are often called blooms, harmful cyanobacteria blooms (HCBs), or harmful algal blooms (HABs). You should learn to recognize cyanobacteria so that you can avoid them and stay safe on the water.

Jump to a specific cyanobacteria topic using these links:

The Vermont Department of Health is your go-to option for information on current cyanobacteria blooms in the state.

Visit the Cyanobacteria Tracker Map for information on blooms near you.

Report cyanobacteria blooms to the Health Department using their easy online form.

A cyanobacteria bloom at the Shelburne Pond VT boatlaunch_2022

A cyanobacteria bloom at Shelburne Pond, VT. Photo: A. Shambaugh

Cyanobacteria are a type of algae that share many characteristics with bacteria. Like many algae, they use photosynthesis to produce their foods. Like bacteria, they have no internal structures, chloroplasts or nuclei. They are ancient organisms – fossilized colonies known as stromatoliths are found around the world. Cyanobacteria are particularly good at growing in warm, nutrient-rich, calm waters but they are also common in pristine lakes. Chances are very good that your favorite lake or pond will have cyanobacteria.

Cyanobacteria are natural and native members of Vermont’s aquatic environment and they have important roles to fill. They feed other aquatic organisms and release oxygen through photosynthesis. Some species can take nitrogen gas from the air through a process called nitrogen fixation. The nitrogen they capture is used by other organisms when cyanobacteria decompose or are eaten. Most of the time, we don’t even notice they are there doing all these good things. We don’t want to eliminate them entirely from our lakes and ponds. It’s probably not possible anyway. Instead, we want to recognize them when they appear and know what we can do to make it less likely that dense long-lasting blooms become an annual event.

We have learned a lot about cyanobacteria biology and how they adapt to many different aquatic environments. We know that they are very good at growing in conditions that other algae and plants can’t tolerate. There are also many things we don’t know – why they form blooms, why they produce toxins, and why we are seeing cyanobacteria more often now. Scientists and lake managers will be studying cyanobacteria for years to come.

Health Concerns About Cyanobacteria

Exposure to cyanobacteria can be a problem. Some can produce potent toxins that affect your liver or nervous system. Some can cause allergic reactions or allergy-like symptoms. Direct contact with cyanobacteria or water containing their toxins is not a good idea. Drinking water that may contain cyanobacteria or their toxins should also be avoided. Breathing in water droplets while on the water or on the shore can also sometimes cause a reaction.

Image of dogs along a lake shoreline. Photo: A. Shambaugh.

Dogs exploring the water’s edge where they can come in contact with cyanobacteria. Photo: Angela Shambaugh

Children and pets are most at risk. They have smaller body weights and happily put things into their mouths that most of us would avoid. Dogs who go swimming and then lick their fur may accidentally eat cyanobacteria. Livestock and wildlife may be at risk if their drinking water sources have a bloom.

If you think that you or someone you know may be having a reaction to cyanobacteria, be sure to call your health care provider right away.

Anyone drawing water from lakes, ponds, rivers, or other surface waters must watch for cyanobacteria too. Most home drinking water purification systems cannot remove cyanobacteria toxins and cyanobacteria themselves can sometimes survive inside the system. Portable water purification systems for hiking and camping may also not be effective for cyanobacteria and their toxins. It is important to check with the manufacturer of any system to see how they handle cyanobacteria. Municipal drinking water systems in Vermont are aware of cyanobacteria. They receive assistance from the VT Departments of Environmental Conservation (VT DEC) and Health (VT DOH) whenever they have concerns regarding cyanobacteria.

Visit the VT DOH Cyanobacteria page to learn more about symptoms of cyanobacteria sickness, testing for cyanobacteria, and other information.

How Do Cyanobacteria Affect Lakes?

A cyanobacteria bloom with floating duckweed on Shelburne Pond, VT.

Cyanobacteria and floating duckweed on Shelburne Pond, VT. Photo: Angela Shambaugh

All lakes and ponds have cyanobacteria. As noted above, they are important members of the food web and help recycle nutrients. As cyanobacteria become more abundant in a lake, however, they can cause significant changes to occur.

A lake or pond with a large variety of aquatic plants, algae, zooplankton, and fish is a healthy one. The number of individuals in each of these groups is strongly connected to the amount of nitrogen, phosphorus, and other nutrients in the water. In general, waters with low nutrient levels, especially of phosphorus, will have fewer individuals. High-nutrient waters can feed many, many individuals. Healthy, diverse high nutrient lakes are hot spots for fishing and wildlife.

Under the right conditions – excess nutrients, warm calm waters – cyanobacteria can grow and grow and grow. Lakes can tolerate an occasional bloom and recover when nutrients or temperature go back to normal. The lake may begin to change if conditions don’t return to normal.

A growing population of cyanobacteria can take the nutrients aquatic plants and other algae need. They shade the water and prevent light from getting to aquatic plants. They aren’t a favorite food for zooplankton. Oxygen levels can drop very low during cyanobacteria blooms. This can lead to fish and mussel kills. People don’t enjoy a lake full of cyanobacteria either. It’s not pleasant to swim in or look at scummy water. It smells. Worse, it can make people and animals sick.

Once cyanobacteria rule, it is hard for a lake to recover. Recovery rarely happens on its own. It takes a lot of money, work, and time to control them. We aren’t always successful. It is far less expensive and overall better for the lake to keep cyanobacteria from getting the upper hand in the first place. This means managing the landscape around the lake and watershed for lake protection. See our Protecting Lakes and Ponds webpage and the resources below for more information on what YOU can do.

How Do We Manage Cyanobacteria?

Oscillatoria spp. Photo: Proyecto Agua,

Oscillatoria spp. Photo: Proyecto Agua,

Management and control of cyanobacteria takes work. These are living organisms that have survived on Earth for millions of years. They have adapted to many different environments – water, soil, and even deserts. Every location has different conditions and biological communities. Experience has shown that there is no single way to prevent cyanobacteria blooms.

In general, long-lived dense planktonic cyanobacteria blooms occur in warm, nutrient-rich waters. Climate change is raising water temperatures around the world, including in Vermont. Nutrient concentrations in lakes are also rising, especially phosphorus. These changes mean that more lakes may be affected by HCBs.

As individuals and communities, we can make choices about land use, property management, and purchases that are part of the solution to slowing climate change and stopping the flow of nutrients into our waters. These are the best available options to reduce the frequency and occurence of cyanobacteria blooms in the long run. Read more about shoreline protection and watershed management activities in other areas of our website.

Image of cyanobacteria filaments with heterocysts

Cyanobacteria filaments with heterocysts. Photo: Bioimages UK at

There are also chemical and mechanical options to reduce the growth of cyanobacteria in the short term. These usually require the skills of a professional lake manager and can be very expensive. They often require state permits and oversight as well.

Here in Vermont, alum treatment in Lake Morey and an aeration system in Lake Carmi have been used to manage cyanobacteria blooms with varying success.

These Interstate Technology and Regulatory Council (ITRC) resources do a deep dive into cyanobacteria ecology, health concerns, and management options. They will help you learn more about steps you might take to slow the growth of cyanobacteria.

  • Strategies for Preventing and Managing Harmful Cyanobacterial Blooms, HCB-1
  • Strategies for Preventing and Managing Benthic Harmful Cyanobacterial Blooms, HCB -2

How Do I Recognize Cyanobacteria?

Cyanobacteria come in many colors and textures. Intense floating blooms of planktonic cyanobacteria can form scums and dense layers on the water’s surface. These can be green, white, or even blue when sunlight begins to destroy their green pigments. Many people mistake harmful cyanobaceria blooms (HCBs) for paint or chemical spills.

Benthic cyanobacteria form dense layers covering the bottom of streams and rivers. They can also grow over plants and rocks. Benthic blooms can be dark green, tan, or blackish. Pieces of the mat can break off and float on the surface or wash onto the shoreline.

These videos can help you learn what cyanobacteria look like.


There are many, many articles and guidance documents focused on cyanobacteria. Here is a short list of local and national materials that may be helpful for you.


  • The VT DOH’s Cyanobacteria Webpage provides general information on HCBs and associated health concerns, guidance on fish consumption and drinking water, links to the Vermont Cyanobacteria Tracker Map and a form for reporting blooms, and links to signage used for identifying lakes and beaches having cyanobacteria.
  • The VT DEC’s cyanobacteria webpage provides general information on cyanobacteria monitoring, the DEC volunteer monitoring program for inland lakes and a YouTube video of their training, and links to DEC resources about lake and small pond management options.
  • The Lake Champlain Committee coordinates volunteer cyanobacteria monitoring in the Champlain Basin along with the Lake Champlain Basin Program, the University of Vermont, and the VT DEC. Their webpage provides detailed photos of cyanobacteria, other algae and plants that may be confused with cyanobacteria, images of jar and stick tests to help recognize cyanobacteria, and a sign-up form for volunteer monitors. Monitors receive weekly email updates with tips and photos to improve their skills at identifying cyanobacteria.


  • The ITRC’s Cyanobacteria Guidance documents and trainings provide general information on cyanobacteria and ecology, a deep dive into cyanobacteria toxins and what we currently know about them, sampling and analysis methods for cyanobacteria and cyanotoxins, and an overview of management and control options including evaluation of several dozen chemical and mechanical approaches. The documents have lots of links to additional online references and resources.
  • The North American Lake Management Society’s Inland Harmful Algal Bloom (HABs) Program links to articles in open-access LakeLine Magazine issues that focus on cyanobacteria, a map of national resources and programs focused on cyanobacteria, and updates on cyanobacteria news.