Editor’s Note: This article is the seventh in a multi-part series exploring the hidden science behind the decline of American lakes and reservoirs. Adapted from an educational video series it aims to equip local communities, lake associations, and municipal leaders with the scientific knowledge needed to demand effective, long-term restoration strategies.
What if the monitoring system being used to protect the Finger Lakes from toxic algae blooms is actually blind to them? What if the most widely used measurement for assessing lake health gets more inaccurate precisely when your lake is in the most danger?
For years, communities across our region have been spending millions on lake management, guided by annual reports that tell them everything is under control. Yet, toxic blooms continue to shut down our beaches and threaten our drinking water.
The reason for this disconnect is not a mystery. It is a fundamental flaw in how we measure lake health – a flaw that has recently been exposed by a landmark scientific study right here in the Great Lakes region.
The 1960s science we still use today
To understand the problem, we have to look at how lake health is measured. In the 1960s, scientists developed the Trophic State Index (TSI) to categorize how degraded a lake had become. A key part of this index is measuring Chlorophyll-a, the green pigment found in all plants and algae.
The logic was simple: more nutrients lead to more algae, which means more Chlorophyll-a. If you measure Chlorophyll-a, you get a quick and easy measurement of algae. For its time, this was good science.
But our understanding of lake ecology has changed dramatically since then. We now know that the bright green scums that produce lethal toxins are not algae at all. They are cyanobacteria – ancient bacteria that can photosynthesize but also produce potent toxins that can sicken humans and kill pets.
Why chlorophyll-a is blind to the threat
This discovery should have triggered a complete overhaul of how we monitor our lakes. But it didn’t. We kept using Chlorophyll-a measurements, assuming they would detect cyanobacteria just as well as beneficial algae. They do not.
Beneficial algae use Chlorophyll-a to photosynthesize, which is why they are green. Cyanobacteria, however, use a different, blue pigment called phycocyanin. They actually have less Chlorophyll-a per cell. Furthermore, the blue pigment interferes with the equipment (fluorometers) used to measure Chlorophyll-a, causing the instruments to under-read the results.
Imagine inventing a device in the 1960s that measures the noise of gasoline engines to calculate highway traffic. It works perfectly for decades. Then, electric cars are invented. As more electric cars hit the road, your device doesn’t hear them. It starts reporting that traffic is decreasing, even as the highway becomes completely jammed. Your device isn’t broken; it is just the wrong tool for the new reality.
This is exactly what happens in our lakes. As toxic cyanobacteria take over and kill off beneficial algae, the Chlorophyll-a readings go down. A lake manager looking at the report thinks the lake is improving, while in reality, it is collapsing into a toxic state.
The definitive proof: The Great Lakes study
The definitive proof arrived in January 2026. A group of EPA-affiliated scientists published a landmark paper in the journal Limnology and Oceanography: Methods. They analyzed ten years of data from 72 monitoring stations across all five Great Lakes, comparing Chlorophyll-a fluorometer readings to actual microscopic identification of the water samples.
Their findings were unequivocal and alarming. They discovered that fluorescence-based measurements systematically fail to detect cyanobacteria. In fact, the measurement could only explain 6% of the variation in cyanobacteria levels. The other 94% was completely undetected.
Even worse, the equipment failed most spectacularly when the danger was highest. In half of the samples where microscopes detected massive, high-density toxic blooms, the Chlorophyll-a monitors registered near-zero readings. The monitoring system was completely silent while the “house was burning down.”
The algaecide trick: Duped into making it worse
Failing to detect a toxic bloom is bad enough, but relying on Chlorophyll-a often leads to a much more destructive outcome: it tricks communities into actively making the problem worse.
When a lake report shows high Chlorophyll-a, a contractor will often recommend applying chemical algaecides. The chemicals are sprayed, the beneficial algae die, and the Chlorophyll-a levels drop. The contractor points to the lower numbers as proof of success.
But scientific research shows that algaecides are highly effective at killing beneficial algae, while cyanobacteria quickly develop resistance. By spraying the lake, you wipe out the harmless competition, leaving the lake wide open for the resistant, toxic cyanobacteria to take over. The Chlorophyll-a readings stay low, hiding the fact that you have just handed the lake over to a toxic super-bug.
Your lake committee’s next Move
The science is clear, and the data from our own Great Lakes region proves it. If your lake association or municipality is relying on Chlorophyll-a or the Trophic State Index to monitor water quality, you are not getting the full picture.
It is time to demand better. Ask your lake managers to provide detailed, taxonomic analysis of the phytoplankton in your lake. You need to know exactly what microscopic life is in the water, not just how green it is. Until we start measuring what actually matters, we will continue to be blindsided by the toxic blooms threatening the Finger Lakes.
