Common Misconceptions Are Keeping Lakes "Sick"

By Dave Shackleton

Long-held misconceptions about lake management fuel the intensity and recurrence of harmful algal blooms.

Harmful algal blooms (HABs) are an escalating concern for both recreational and municipal water bodies. Driven primarily by nutrient enrichment and rising temperatures, HABs — caused by toxin-producing cyanobacteria — pose a significant threat to lake health, public safety, and water infrastructure.

Cyanobacteria are highly adaptable organisms that thrive in stagnant, nutrient-rich, and warm environments. As these conditions become more common, blooms are appearing earlier in the season, lasting longer, and covering larger surface areas. In many regions, what were once sporadic or seasonal events are now near-permanent features of the aquatic landscape.

Moreover, recent blooms are demonstrating higher concentrations of cyanotoxins, increasing the risk to human and animal health. These more toxic and widespread blooms place additional strain on drinking water treatment systems, raise public safety concerns, and complicate lake management strategies.

Without long-term strategies focused on prevention and ecological balance, the risks to both environmental and public health will continue to intensify.

Commonly held misconceptions about how to manage algae blooms are effectively keeping lakes “sick” by facilitating the dominance of cyanobacteria and accelerating the deterioration of the lake’s ecosystem.

These challenges range from a long-held belief that chemical interventions are an effective solution, as well as misconceptions about the root causes of HABs, and even confusion over the metrics used to assess lake health.

These misconceptions highlight the true root causes, such as hypoxia, sediment accumulation, and nutrient recycling, and promote more effective, natural, chemical-free management strategies.

MISCONCEPTION: Chemical Applications Effectively Control HABs

The most common conventional approaches to addressing invasive weeds and algae blooms typically rely on the use of treatment chemicals.

However, biocides (herbicides and algaecides) as well as chemicals designed to reduce phosphorus levels accelerate the deterioration of the reservoir’s ecosystem while increasing the frequency and intensity of HAB events.

Algaecides

Algaecides are chemicals specifically formulated to kill algae, including cyanobacteria. While effective, the side effects of the process are what keep lakes sick. In fact, over time, the use of algaecides accelerates the onset of toxic HABs and intensifies them.

Algaecides, specifically, have been proven to be more effective against beneficial algae than against toxic cyanobacteria. By killing algae and cyanobacteria cells, toxins are released that lead to the destruction of more beneficial organisms. The dead algae cells also sink to the sediment and, as they decompose, recycle nutrients to fuel more algae blooms. This decomposition causes oxygen to be consumed in the water, leading to hypoxic conditions, or “dead zones,” where aquatic life cannot survive.

Over time, the continued application of algaecides causes compounds — the sediment-nutrient stockpile at the bottom of a lake that are recycled to feed more algae blooms and shift the profile of the phytoplankton towards more and more cyanobacteria.

Herbicides

Herbicides are applied to manage invasive or nuisance aquatic weeds growing in the nutrient-rich sediment. Like algae, dead weeds sink to the sediment and decompose, contributing to oxygen depletion and fueling more algae blooms.

Other secondary effects of herbicides include habitat loss and ecosystem imbalance. They can even pose risks to human and wildlife health, especially in drinking or recreation waters.

Alum And Other Phosphorus Precipitants

Alum and other phosphorus precipitants are chemical agents used to reduce the levels of total phosphorus (TP).

Alum, short for aluminum sulfate, is the most used of these compounds. Other precipitants, such as ferric chloride or ferric sulfate (iron-based), and calcium compounds like lime, function similarly by chemically binding phosphorus and precipitating it out of the water, down into the sediment.

The logic is reasonable: Take phosphorus out of the water that cyanobacteria use as a nutrient source.

Precipitants deposit phosphorus into sediment. When sediment is hypoxic, the microbiology changes and recycling of nutrients accelerates. Beneficial algae cannot access them there, because they can only float passively near the surface. Cyanobacteria can control their buoyancy and descend to the sediment to use those nutrients, so precipitating phosphorus into the sediment helps cyanobacteria become even more dominant over time.

In short, lake management reports that tout the killing of algae with algaecides and weeds with herbicides are not telling the whole story.

“[C]hemical and physical methods either dampen the effects of a bloom or shorten the bloom, but do not prevent the bloom,” says Wayne Carmichael, PhD, a prominent expert in aquatic toxicology, known for his work on toxic cyanobacteria. He adds that the net effect is often only a temporary improvement of lake conditions for a few weeks or months.

MISCONCEPTION: There Are No Visible Algae Blooms And Aquatic Life Is Evident, So The Lake Must Be Healthy

A common misconception in lake monitoring is the reliance on surface-level measurements of dissolved oxygen to assess overall water quality.

While surface readings may appear normal, they provide no indication of the oxygen conditions at depth where the most serious problems originate. Hypoxia, or low oxygen levels, begins in the deeper layers of a lake due to decomposition of organic matter, which causes sediment-nutrient accumulation. These conditions go undetected when monitoring is limited to the upper water column.

As a result, stakeholders may develop a false sense of security, unaware that the lower strata are highly hypoxic — an environment that supports internal nutrient recycling and fuels the proliferation of HABs.

Other indicators, such as evidence of aquatic life, can be misleading.

If fish are being caught only in the upper levels of the lake, it may be because the deeper waters are hypoxic and all the fish are being forced up to shallower water that is still oxygenated, making them easier to catch.

MISCONCEPTION: Nutrient Inflows Are The Primary Problem

A common misconception in lake management is the belief that nutrient inflows from the watershed are the primary issue, and therefore, financial and operational resources should be concentrated exclusively on mitigating these external sources.

These external sources of nitrogen and phosphorus include agricultural runoff, sewage, stormwater, septic systems, groundwater, and atmospheric deposition that run into the lake.

That issue likely passed decades ago. In many lakes, it is the internal sources that contribute more nitrogen and phosphorus to algae blooms. The threat is from the decades of accumulated phosphorus and nitrogen stored in the organic sediment.

These act like a high-risk “time bomb” that is released under low-oxygen or stratified conditions, particularly during warmer months.

Lake Honeoye, one of the Finger Lakes in upstate New York, is a textbook example. Despite significant and expensive efforts to eliminate nutrient inflows from its watershed, persistent HABs worsen every year.

When the lake’s deep-water oxygen levels drop below 1.0 mg/L, sediment-bound phosphorus is released into the water column. This internal recycling becomes a self-sustaining driver of eutrophication and recurring HABs.

MISCONCEPTION: A Good Trophic State Index Score Means The Lake Is Healthy

For the past five decades, the Trophic State Index (TSI) has served as a standardized eutrophication assessment, but it has significant limitations and redundancies.

The traditional TSI, which was developed in the 1970s by Robert E. Carlson to quantify nutrient-driven productivity in lakes and reservoirs, only measures and correlates symptoms and gives little indication of conditions at depth, which is where the root causes of the problems play out.

The narrow emphasis on symptoms has led to many misguided lake management practices. This includes reactive, short-term actions such as the use of algaecides and phosphorus precipitants that temporarily improve TSI scores but ultimately worsen the underlying causes and hasten the development of HABs.

A more effective approach to assessing lake health involves quantifying the volume of hypoxic water to evaluate the extent of oxygen-depleted zones within the reservoir, combined with continuous phytoplankton monitoring to track the balance between beneficial algae and harmful cyanobacteria.

These factors can be systematically monitored using the Reservoir Risk Assessment and Tracking System (RRATS), which consolidates the data into a streamlined Reservoir Risk Index score.

This score provides a clear and actionable indicator of a reservoir’s current risk status. Only with this foundational understanding can lake managers effectively prioritize interventions, allocate resources strategically, and implement early risk mitigation measures.

From Misconceptions To Meaningful Solutions

Decades of misconceptions have led to lake management strategies that often treat symptoms rather than root causes. As a result, many lakes continue to decline despite costly and well-intentioned interventions. Misguided reliance on chemical treatments, surfacelevel oxygen readings, and outdated metrics has created a cycle of temporary improvements followed by worsening conditions.

By addressing the true root causes of water quality decline — such as sediment-bound nutrient release and oxygen depletion — lake managers can move beyond reactive, short-term fixes. With a more holistic and preventative approach, supported by better data and monitoring tools, the path to healthier, more resilient lakes becomes not only clearer but also achievable.

About The Author

Dave Shackleton is the president of Clean-Flo International, a U.S.- based leader in biological water management solutions for lakes, reservoirs, rivers, and wastewater treatment facilities.