Cyanobacteria in Our Lakes
Cyanobacteria blooms are an increasing concern in New Hampshire’s lakes, with implications for public health, ecosystem integrity, and property values. These harmful blooms, fueled by excess nutrients and warming temperatures, have become common in many waterbodies across New Hampshire. While cyanobacteria are naturally present in lakes, certain conditions - such as heavy rain events or sediment disturbance that release nutrients into the water, followed by warm weather - can trigger rapid and potentially toxic growth.
Photo by NH Lakes
Fortunately, cyanobacteria blooms remain rare in Lake Sunapee, which continues to support exceptionally high water quality. But this is not guaranteed. Protecting the lake requires a shared commitment to watershed stewardship: minimizing fertilizer use, maintaining functioning septic systems, and planting native vegetation along shorelines all play a critical role in reducing nutrient pollution and preserving the lake’s resilience in a changing climate.
Gloeotrichia bloom in Lake Sunapee. Photo by Midge Eliassen
What are Cyanobacteria?
Cyanobacteria, formerly known as blue-green algae, are some of the oldest, naturally occurring organisms on Earth. They are photosynthesizing bacteria that are commonly classified as algae (though they are not actually algae) and found in freshwater ecosystems.
They are a normal part of healthy lake ecosystems; presence ≠ bloom
Blooms can produce toxins harmful to people, pets, and wildlife
Different types of cyanobacteria respond differently to temperature, nutrients, weather, and other lake conditions.
There are many kinds of cyanobacteria; they don't all look alike, and not all are harmful. The size and shape of a cyanobacteria colony vary by species. A common one in Lake Sunapee that is visible to the naked eye is called Gloeotrichia echinulata or Gloeo for short. Gloeo form colonies about the size of a pinhead (about 1.5 mm or 1/16 inch) and are light yellow-green. The bloom looks like a surface scum that can range from yellow-green, bright green, to slightly blue-green. Other common cyanobacteria are not visible to the naked eye until they form a bloom.
Click here for an informational packet about cyanobacteria made by the 2026 LSPA-Virginia Tech Calhoun Fellows.
Cyanobacteria Monitoring in the Lake Sunapee Watershed
With support from Maura Beatty, a Burkehaven Fellow with LSPA during the summer of 2026, and a research grant from the Farmer Lian Family - which funded Dartmouth researcher Dr. Jess Trout-Haney, the developer of this project's protocol and who trained Maura and the water quality interns - LSPA established a protocol to analyze cyanobacterial patterns in the watershed throughout the summer and across multiple years. This advancement enhances our capacity to forecast and manage cyanobacterial conditions in the lake.
Across 11 sites and 4 waterbodies within the Lake Sunapee Watershed, Maura was able to help establish a baseline for monitoring changes in cyanobacterial populations over time by collecting and analyzing hundreds of water samples and conducting cell counts, measuring photosynthetic pigments, and testing toxin levels.
It is important to get this baseline because increased nutrient loading and warming temperatures could mean that over time we may begin to see a greater abundance of cyanobacteria and harmful algal blooms. We are beginning monitoring now so that we can track this change over time. Long-term monitoring allows us to see and respond early if a trend emerges spatially, temporally, or in overall abundance.
The red dotted line above shows where today’s cyanobacteria abundance falls (~12% mean relative abundance) in the 2036 hypothetical graph (~42% mean relative abundance).
To learn more about Maura and Jess’ work, click to view their recorded presentation about Understanding Cyanobacteria in Lake Sunapee: Monitoring and Research.
What You Can Do to Help Prevent Toxic Blooms
For detailed information about actions homeowners can take to protect water quality and prevent cyanobacteria blooms, see our Watershed Wise Resources page
Eliminate the use of fertilizers on your lawn and garden or use phosphorus-free products (the middle number on a fertilizer bag should be 0)
Pump your septic tank every three years and have the whole system inspected, especially if it’s an older system
Plant trees and shrubs along the water’s edge if you own shorefront property
Direct stormwater from driveways and roofs into forested areas, rain gardens or stormwater systems
Dispose of pet waste properly
Click here to download LSPA’s informational card on cyanobacteria.
If You Suspect a Bloom
If you see a possible cyanobacteria bloom, please call LSPA right away at 603-763-2210 so we can take a look and collect a sample if necessary. Be prepared to provide the exact location and a detailed description of what you are seeing.
You can also report your sightings directly to NHDES through their online bloom report form.
*If you see anything suspicious we recommend that you stay out of the water and keep your pets out too.
Cyanobacteria harmful algal blooms (CyanoHABs) can look very different. Cyanobacteria can look like scum, mats, spilled paint or paint chips. The color of the water can turn blue, green, white, yellow or brownish. - NHDES
Cyanobacteria Look-Alikes
Pine Pollen
Pollen
Pollen grains are small and close together. Wind can blow them near the shoreline where they aggregate and form smoky wispy "clouds.”
Green Filamentous Algae
Cotton candy-like masses that are often green or yellowish in color and are seen free-floating in the water column or attached to sticks and other debris.
NHDES suggests to determine if it’s filamentous algae or cyanobacteria to perform a stick test. “Grab a stick and attempt to lift the mass out of the water. If it stays on the stick when lifted out of water and appears as a bundle of green slimy threads of hair, it is most likely green filamentous algae. If it disperses and clouds the water, and you cannot easily lift a bundle, then it could be cyanobacteria.”
Click here to read more about Green Filamentous Algae from NHDES.
Other Cyanobacteria Resources
NH’s Cyanobacteria Plan: A Statewide Strategy - This plan includes key strategies and goals to address the increase of cyanobacteria blooms in New Hampshire's lakes and ponds and eventually control them in our waters.
NHDES Harmful Algal Blooms (HABs) page
Healthy Swimming Mapper - See locations of current cyanobacteria warnings or watches on a map from NHDES.
Waterbody Specific Cyanobacteria Warnings- Sign up for updates from a specific waterbody.
Cyanobacteria Self Risk Assessment - Learn more about risk associated with HABs, and how to mitigate your personal risk in this short video by NHDES.