Alage - Charles River Watershed Association

What are Cyanobacteria?

Cyanobacteria, or blue-green algae, are photosynthetic bacteria that live and grow in aquatic environments. One of the common cyanobacteria found in the Charles River is Microcystis, which grows naturally in calm, warm, shallow water that is rich in nutrients like nitrogen and phosphorous.

When present in large numbers, these organisms can give the water a green, paint-like appearance (see image above) and can produce toxins which are harmful to humans, dogs, and other mammals in large doses.If you see water that looks bright green or contains bright green strands, avoid contact with the water as much as possible and wash contacted areas after exposure.

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Cyanobacteria Causes

A combination of factors, such as excess nutrients like phosphorus and nitrogen, warm temperatures, and sunlight encourage blue-green algae growth. In the Charles, severe cyanobacteria blooms are usually caused by heavy rainstorms that bring an enormous influx of nutrients to the river, followed by hot weather that leads to warm water temperatures, thus creating perfect conditions for cyanobacteria growth. Direct discharges of heated water likely contribute to cyanobacteria growth as well.

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Concerns Associated with Cyanobacteria

Algae - Charles River Watershed Association

The Massachusetts Department of Public Health defines a cyanobacteria bloom as the presence of any of the following:

  • Cyanobaceria concentrations >70,000 cells/ml of water
  • Cyanotoxin levels >14 parts per billion (ppb)
  • Visible presence of cyanobacteria scum or mat

When cyanobacteria die and begin to decompose, they secrete a toxin, and accumulations of this toxin can pose a health risk to humans and animals. Common reactions to these toxins include skin rashes, eye irritation, and possible gastrointestinal distress. Additionally, blue-green algae become a serious problem when it grows in abundance, preventing light and oxygen from getting into the water, thus shading and smothering other aquatic organisms.

Unfortunately, there is no direct correlation between visible algae in the water and toxin levels, so it can be difficult to determine when the water is safe. 

If you see water that looks bright green or contains bright green strands, avoid contact with the water as much as possible and wash contacted areas after exposure.

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Monitoring Cyanobacteria In the Charles River

CRWA’s cyanobacteria monitoring program identifies potentially harmful cyanobacterial blooms and works with state and local agencies to inform the public of confirmed blooms. Since 2014, the program has also contributed data to the U.S. Environmental Protection Agency’s (EPA’s) Cyanobacteria Monitoring Collaborative, which has developed and tested low-cost, user-friendly methods for identifying cyanobacteria and detecting cyanobacterial blooms. Local schools, universities, and members of the general public are encouraged to participate in the app-based bloomWatch project or microscope-based Cyanoscope project. The bloomWatch app is available on Google PlayTM or on the App Store.

Get it on Google Play


On a weekly or bi-weekly basis, CRWA conducts water quality testing for cyanobacteria at three sites in the lower Charles River Basin: Charles River Canoe and Kayak in Kendall Square, Community Boating, and the MIT sailing pavilion. Other locations are monitored on an as-needed basis. At each location, CRWA collects a water sample from the top meter of water and uses a fluorometer to measure the concentrations of the pigments phycocyanin and chlorophyll a, indicators of the abundance of cyanobacteria present. All photosynthetic organisms, including cyanobacteria and green algae, produce chlorophyll a. Only cyanobacteria produce phycocyanin.

You can view real-time levels of chlorophyll a and phycocyanin near the Museum of Science from EPA’s Charles River Buoy.

CRWA also records water temperature and weather conditions at our monitoring locations. The remainder of each sample is stored in a dark plastic bottle and kept frozen. At the end of the field season, CRWA thaws and analyzes the frozen samples for chlorophyll a and phycocyanin. Freezing the samples allows participants in the Cyanobacteria Monitoring Collaborative to standardize our sample handling procedures and share our data with EPA to help identify large-scale trends in the occurrence, distribution, and duration of cyanobacterial blooms.

When CRWA observes bluish-green clumps or scum or high levels of phycocyanin in the water, or receives a report from the public, we submit a report of a potential cyanobacteria bloom to the Massachusetts Department of Public Health (MDPH). MDPH responds to reports of potential cyanobacteria blooms by sending someone to the location of the potential bloom to collect a water sample. A certified laboratory then counts the number of cyanobacteria that are present in the sample. If there are more than 70,000 cells of cyanobacteria per milliliter of water, MDPH will recommend that the agency responsible for the affected waterway, either the Massachusetts Department of Conservation and Recreation or the city or town Board of Public Health, issue a public health advisory. Follow-up monitoring is then conducted on a weekly basis until cyanobacteria concentrations fall below state guidelines for two consecutive weeks. Read more about the history of cyanobacterial blooms on the Charles River here.

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Preventing Cyanobacteria in the Charles

While there are currently no recognized methods to eliminate the cyanobacteria from the water, blooms can be prevented by reducing the river’s nutrient levels and water temperature. CRWA has developed several projects to help monitor and address cyanobacteria growth in the Charles River:

Water Quality Monitoring - CRWA manages a team of over 80 volunteers, or citizen scientists, who monitor multiple sites along the Charles River and collect water samples, measure depth and temperature, and record river conditions. This data is used to identify problems in the river and trends in water quality, and to track the progress of efforts to clean up the Charles. 

Blue Cities Initiative - CRWA designs and advocates for green infrastructure systems, like rain gardens and permeable pavement, to treat stormwater runoff naturally before it enters the Charles - all while enhancing neighborhoods and connecting existing open spaces.

Environmental Advocacy - Through reforming state water law, policy and practice, CRWA works to protect aquifers and maintain streamflow, and to prevent excessive discharges of hot water into the river.

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READ: Kendall Plant to Eliminate Thermal Pollution in the Charles River

Stay Informed of Charles River Water Quality

Every year from July through October, CRWA provides daily water quality alerts of the Charles River lower basin, through our Water Quality Notification Program. Also known as the “Flagging” Program, CRWA and participating boathouses provide daily flag colors based on bacteria levels, cyanobacteria counts, and rainfall-based prediction models.

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Sign up for Daily Water Quality Alerts

Learn More About the Charles River

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