Morning Swim: The Hidden Microbial World of Freshwater Lakes
- Heather McSharry, PhD
- 2 days ago
- 16 min read
Summary
A quiet morning at the lake feels peaceful and unchanging—but beneath the surface, an invisible world is constantly responding to sunlight, wind, temperature, wildlife, and even our own activities.
In this episode, we'll scratch the surface of the fascinating microbial ecology of freshwater lakes, from the harmless bacteria that help sustain aquatic ecosystems to the few organisms that occasionally affect human health. You'll learn why swimmer's itch is really a case of mistaken identity, how cyanobacterial blooms develop, why Naegleria fowleri infections are extraordinarily rare, and how environmental conditions influence the microbes living around us.
We'll also look at how scientists monitor recreational waters, why changing weather patterns are becoming increasingly important to public health, and how citizen scientists are helping researchers better understand the lakes and rivers we love.
This episode invites you to see lake microbes as part of a living ecosystem that has been quietly shaping our planet for billions of years. The next time you're standing beside a lake at sunrise, you'll know there's far more happening beneath the surface than meets the eye.
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Citation List at the end of the post
It's just before sunrise. The lake is still half asleep. Mist drifts low across the water, softening the shoreline until the trees seem to fade into it. Somewhere farther down the bank, a loon calls once before everything settles back into silence.
A family arrives carrying towels over their shoulders. Someone unfolds a pair of lawn chairs as a cooler thumps onto the ground. A little boy has kicked off his shoes before the rest of the family has even finished unloading the car. His feet splash through the wet sand. And before anyone can tell him to wait... he's in. The surface ripples outward in widening circles as he begins to swim.
Lots of summer mornings begin like this at a lake somewhere. We see cool water at sunrise as a welcome escape from another hot day before the throngs of people arrive.
But the throngs aren't only on the shore. The lake itself is bursting with life.
This is Morning Swim: The Hidden Microbial World of Freshwater Lakes
Why We Swim
OK, so people have always gathered wherever water offered relief. And for me this is so true. I love swimming. I mean, aside from skydiving, body surfing feels the closest to flying. And I adore a nice shoreline. Which is where we start here. And as we move from the shoreline, to the warm shallows, to the deeper water, we'll meet a few of the organisms that share these places with us.
So let's kick off our shoes and dip our toes in right at the water's edge.
The Hidden Ecosystem
Wherever land and water meet there's a rich environment for plants, insects, birds, fish, snails, amphibians, and countless microscopic organisms. Sunlight reaches the bottom, aquatic vegetation grows thickly, and nutrients wash in from the surrounding landscape. It's full of life. And where there's abundant life, there are relationships, like predators and prey, or hosts and parasites, all carrying on exactly as they've evolved to do. One of those relationships occasionally includes us.
Have you ever heard of something called swimmer's itch? Sounds fun.... It turns out it's
the accidental result of a parasite getting confused about who its host is. sThe condition—officially called cercarial dermatitis—is caused by microscopic larvae of parasitic flatworms called avian schistosomes, or bird blood flukes.
Normally, these parasites have a pretty specific life cycle involving waterfowl like ducks, geese, and other aquatic birds, along with freshwater snails. Eggs released by infected birds hatch into tiny larvae that infect snails. Inside the snail, they develop into another free-swimming stage called cercariae, which are released into the water by the thousands each day and go searching for a bird to complete the cycle.
Humans aren't on the guest list...but sometimes we accidentally wander into the party.
When these microscopic larvae encounter a swimmer instead of a duck, they mistake us for the right destination. They're attracted to things like body heat, movement, and chemicals on our skin, so we seem close enough. They penetrate the outer layers of our skin, but because humans aren't the right host, they can't survive or continue developing. They quickly die, and it's actually our immune system reacting to those tiny invaders that causes the problem.
The result is an intensely itchy rash that can appear within hours—or sometimes up to a day—after swimming. You might notice small red bumps or itchy welts, and while the rash usually clears up within about a week, the itching can be pretty miserable. Interestingly, people who are exposed repeatedly can sometimes have even stronger reactions because their immune system becomes more sensitive over time.
Children are often affected more than adults, partly because they spend more time splashing in the shallow water where aquatic plants grow and where the snails that host these parasites are most abundant. They also tend to stay in the water longer and are less likely to towel off immediately after getting out, which may slightly reduce the chance of any larvae remaining on the skin long enough to penetrate.
The good news is that you don't need antiparasitic medication because the parasites die almost immediately in human skin. Treatment is really about relieving the itching with things like cool compresses, calamine lotion, antihistamines, or hydrocortisone cream.
And despite what you might think, swimmer's itch doesn't mean the lake is dirty. In fact, many fresh water beaches routinely test for bacteria like E. coli, but they don't usually monitor for these parasites because they're much harder to detect. Swimmer's itch is just the result of a naturally occurring wildlife parasite whose life cycle occasionally intersects with ours.
So...it's not a reason to avoid lakes altogether. It's just one of those strange little reminders that nature doesn't always realize we're not ducks.
Oh and if you've ever come home from warm coastal ocean playtime with an itchy rash, like my son did after surf camp in the Gulf of Mexico, that's not this. That was 'sea lice' which are actually tiny jellyfish or sea anemone larvae whose stinging cells irritate the skin. They are found in a lot of warm coastal waters and are no fun because they get caught between your suit and your skin.
Ancient Blooms
OK, as we move away from the shoreline, the shallow coves of a lake often look inviting.
The water warms quickly and the surface becomes glassy. Children can still touch the bottom, so it's the perfect place to float on an inflatable raft while dragonflies skim across the water.
Under certain conditions, though, these same quiet coves can become ideal habitat for cyanobacteria. Despite their common nickname—blue-green algae—cyanobacteria aren't actually algae. They're ancient photosynthetic bacteria that have been on Earth for more than 2.5 billion years. In fact, scientists credit their ancient ancestors with producing much of the oxygen that transformed Earth's atmosphere long before animals or plants ever existed. And most of the time, they're just a normal and important part of a healthy aquatic ecosystem.
But when you get a confluence of warm temperatures, abundant nutrients, calm water, and plenty of sunlight, these organisms can multiply rapidly, creating what's called a bloom. Those nutrients I mentioned often come from fertilizer runoff, animal waste, decaying vegetation, or could have accumulated naturally in lake sediment over time.
Some of these blooms are harmless, but some produce toxins—especially compounds called microcystins—that can affect people, pets, livestock, and wildlife. Interestingly, even species capable of producing toxins don't always do so, and scientists still don't completely understand why one bloom becomes toxic while another doesn't. Unfortunately, there's no reliable way to tell just by looking at the water. If you've ever seen a lake that looks like someone spilled green paint across the surface, or noticed thick floating mats that resemble pea soup, you've probably seen a cyanobacterial bloom. But these blooms don't all look the same. Some look like turquoise streaks, floating clumps, or even a thin film of paint on the water.
And something I find fascinating is that wind can also play a role in these. Because many cyanobacteria float near the surface, a steady breeze can push them toward one shoreline or into a sheltered cove. That means one side of a lake may look perfectly clear while another has a dense bloom.
OK, so many—but not all—popular recreational lakes are monitored throughout the summer because blooms can develop quickly, especially during extended periods of hot, calm weather. And if toxin levels become elevated, swimming advisories or temporary beach closures may be issued until conditions improve.
But please keep this in mind: a lake doesn't have to look obviously green to deserve caution. Sometimes toxins can remain in the water even after a visible bloom has broken apart. That's one reason health officials recommend paying attention to posted advisories rather than only relying on appearance. And keep in mind, although cyanobacteria aren't actually algae, cyanobacterial blooms are commonly referred to as harmful algal blooms, or HABs.
And dogs deserve a special mention here. Dogs chase sticks, bite at floating mats, drink from the shoreline, and then lick their fur after swimming. All of those behaviors can expose them to much higher amounts of cyanobacterial toxins than most human swimmers. Because of that, severe poisonings have occurred after dogs came into contact with toxin-producing blooms. It's one reason veterinarians encourage pet owners to pay close attention to posted advisories before letting dogs enter lakes during the summer.
Most days, of course, none of this is happening. Historically, most lakes never experience significant toxic blooms. Even lakes that do occasioanlly get these, are perfectly safe for recreation much of the year . The point isn't that every patch of green water is dangerous. It's that environmental conditions can change, and with them so can their associated microbial communities.
Amoebas on the Brain
As we continue moving outward from shore, the bottom drops away beneath us, the
water becomes cooler, and the shoreline disappears behind us. And somewhere below, buried in the sediment, lives perhaps the most famous microorganism associated with freshwater swimming: Naegleria fowleri.
Few microbes have acquired a more frightening reputation. Headlines often call it the "brain-eating amoeba." And, while technically describing what happens during infection, that phrase creates an image that's far more terrifying—and far less informative—than the biology itself.
Naegleria is a free-living amoeba. It isn't a parasite waiting for people or hunting brains. In nature, it spends its life feeding on bacteria in warm freshwater and the sediments at the bottom of lakes, ponds, slow-moving rivers, and hot springs. In fact, it's what's known as a thermophilic organism, meaning it thrives in warm water, especially during the hottest parts of the summer.
Its life is surprisingly ordinary. Depending on environmental conditions, it exists in three forms: a hardy cyst that helps it survive unfavorable conditions, a trophozoite, which is its active feeding stage, and a temporary flagellated form that helps it move through the water. It's only the trophozoite—the feeding stage—that can infect humans.
Humans, however, are not part of its normal life cycle. In fact, we're considered a biological dead end and infection with this guy really is extraordinarily rare. Millions of people swim in warm freshwater every year, yet in the United States, only a handful of infections are typically reported annually.
For an infection to occur, several unlikely events have to line up. The amoeba must be present. Water containing the organism must be forced high into the nose. From there, the trophozoite can travel along the olfactory nerve to the brain. Snwallowing lake water doesn't cause infection. Neither does getting water on your skin.
That's why many reported cases involve activities like diving, jumping into warm freshwater, water skiing, or vigorous underwater play—situations where water is driven forcefully into the nasal passages. Stirring up bottom sediment may also increase exposure because that's where the amoeba is often most abundant.
Although infections are most often associated with natural warm freshwater, there have been a few unusual exceptions. In Texas, for example, one infection was linked to a municipal splash pad where inadequate water disinfection allowed the amoeba to survive. Properly maintained, chlorinated pools and splash pads do not provide suitable conditions for Naegleria, making these situations exceptionally rare.
Geography is also important. Historically, most infections in the United States have occurred in the South, where warm freshwater temperatures persist for much of the summer. But as water temperatures change over time, environmental conditions favorable for Naegleria have been documented farther north than in previous decades, and isolated cases have occasionally occurred in places where they once would have been considered highly unusual.
Even so, the risk to any individual swimmer remains extraordinarily low.
Although doctors treat these infections aggressively with multiple medications—including the antiparasitic drug miltefosine—the disease remains one of the deadliest known infections. That's why understanding how infection occurs is so important.
The good news is that there are simple ways to reduce an already tiny risk. Avoid forcing warm freshwater high into your nose, especially during activities like diving or jumping into shallow water. Some people choose to wear nose clips during water sports, and avoiding stirring up sediment in very warm, shallow areas may further reduce exposure.
And one quick clarification: if you remember the widely reported Seattle case involving a woman who became infected after using tap water in a neti pot, that wasn't Naegleria. It was a different free-living amoeba called Balamuthia mandrillaris. The two organisms can both cause rare, serious brain infections, but they live in different environments and have different routes of exposure.
But it's a good reminder for anyone who uses a neti pot or other nasal rinse device, your doctor will confirm that you should use only distilled or sterile water, or tap water that has been boiled and then cooled, to avoid introducing microorganisms into the nasal passages. It's a simple precaution that makes nasal irrigation much safer.
So why begin this series at sunrise?
Because the lake we're standing beside now isn't quite the same lake it will be this afternoon. The change is subtle...almost impossible to notice if you're hanging out enjoying the day. But from the perspective of the organisms living there, morning is a time of transition.
As the sun rises higher, sunlight penetrates deeper into the water. The surface begins to warm while cooler water remains below. Gentle breezes create ripples that mix some layers while leaving others quite stable. Even over the course of one day, sunlight and wind continually reshape the lake's temperature, oxygen levels, and mixing. Fish move between depths. Aquatic birds arrive to feed. Insects emerge from the water while others return to lay their eggs. The lake is constantly responding to forces both visible and invisible, like light, temperature, wind, and the rhythms of the day.
Even the chemistry of the lake begins to change with the rising sun. Throughout the night, fish, aquatic plants, and countless microorganisms continue to respire, consuming oxygen. But photosynthesis stops once the sun goes down. That means dissolved oxygen is often at its lowest point just before sunrise. Then daylight returns, and millions upon millions of microscopic organisms—including algae, cyanobacteria, and aquatic plants—begin photosynthesizing. They quietly release oxygen back into the water while drawing carbon dioxide from it, subtly changing the chemistry of the lake. By afternoon, the very same water can contain considerably more oxygen than it did at dawn, even though to us it looks the same.
The microbes themselves are changing, too. Some organisms thrive as the water warms while others become less active. Ultraviolet radiation from the sun can damage certain microorganisms near the surface, while others find refuge deeper in the water or beneath suspended particles. Some microscopic algae and cyanobacteria can even adjust their position in the water column, moving higher or lower as light conditions change. Tiny animals called zooplankton perform one of nature's remarkable daily migrations, rising toward the surface under the cover of darkness to feed before retreating into deeper water as daylight returns.
Then we arrive.
By midmorning, children are splashing in the shallows. Kayaks leave small wakes across the surface. Boats churn deeper water. Dogs leap from docks. Sand and sediment are stirred into the water along the shoreline. That sediment isn't just dirt—it's home to bacteria, fungi, protozoa, and nutrients that become mixed back into the water when it's disturbed. Wind does something similar on a larger scale, redistributing heat, oxygen, nutrients, and microorganisms from one part of the lake to another.
Those forces shape the environment and are neither inherently good nor bad.
Every hour brings subtle changes and by the time our family packs up their towels around lunchtime, they've spent the morning in a lake that has been quietly transforming around them the whole time.
The Bigger Picture
If there's one thing today's journey into the lake has shown us, it's that microbes respond to the same environmental conditions that shape every other form of life. Things like sunlight, wind, water movement, wildlife, and seasons changing all influence which organisms thrive and which remain in the background. A lake in early May is not the same lake in late August. A calm, hot week creates different conditions than a cool, windy one. Even two coves separated by a few hundred yards may support surprisingly different microbial communities.
That's why public health thinks of recreational water in terms of changing conditions. Around the world, scientists and public health officials keep watch over recreational waters. They test for signs of fecal contamination, monitor harmful algal blooms, investigate fish kills, and issue advisories when conditions become unsafe. The exact methods vary from place to place, but the goal is the same: to understand when environmental conditions temporarily increase the likelihood of certain hazards so people can make informed decisions about how they enjoy the water. Most of the time, the lake is open and the water is inviting. But sometimes, heavy rainfall can wash more bacteria into it or a prolonged heat wave encourages a cyanobacterial bloom. Or maybe a hurricane-induced flood compromises water quality for a few days.
Understanding environmental conditions is a part of safely enjoying nature and as we look ahead, environmental conditions are becoming an increasingly important part of infectious disease surveillance.
Scientists are paying close attention to changing recreational water seasons, expanding periods of warm surface temperatures, and the ways weather patterns influence microbial ecology. In some regions, lakes now remain warm enough for longer portions of the year than they did decades ago. In others, heavier rainfall events temporarily alter water quality in ways that affect recreation.
None of those observations predict the same outcome everywhere, but together, they're reminders that infectious disease doesn't exist apart from the environment.
Citizen Science
One of the most exciting developments has been the growing partnership between researchers and the public. Citizen scientists help report harmful algal blooms. Boaters, anglers, and swimmers submit observations that help environmental agencies identify changing conditions more quickly. Volunteers collect water samples. Communities participate in monitoring programs that improve our understanding of local lakes and
rivers. I got to be a volunteer for the state of Hawaii for a day and take water samples around the island of Kaho' olawe as part of a Hawaiian Island ecology class aboard the 84 ft schooner Dariabar, with the inimitable Dr. Urmas Kaldveer who was an incredible marine biologist and human. We lost him in 2019 and I amso lucky I had that experience. My son and I did this with a soil sampling program and it was so much fun! It's one of the most
effective ways of bolstering our public health systems.
Every place we love has an ecology all its own, and the more we understand those invisible worlds, the better we become at sharing them safely and responsibly.
An organization called SciStarter is a great resource for finding citizen scientist
opportunities near you. https://scistarter.org/
And here are a few water-focused citizen scientist opportunities:
Freshwater and Water Quality
EarthEcho Water Challenge (Global)
Website: https://www.monitorwater.org/
Volunteers test local streams, rivers, lakes, and ponds for basic water quality (temperature, pH, dissolved oxygen, turbidity, etc.) and upload their observations.
Data are shared globally and used for education and long-term environmental monitoring.
Secchi Dip-In (Global)
Website: https://www.nalms.org/secchidipin/
Participants use a simple black-and-white Secchi disk to measure water clarity in lakes.
Water clarity is a useful indicator of algae, sediment, and overall lake conditions.
Thousands of lakes have been monitored through this long-running program.
Texas Stream Team
Website: https://www.tceq.texas.gov/waterquality/nonpoint-source/projects/texas-stream-team
The core statewide network operating across Texas watersheds and local partner groups.
Trained more than 11,000 volunteers to help monitor water quality across the state's 191,000 miles of rivers and streams.
Florida LAKEWATCH
Website: https://lakewatch.ifas.ufl.edu/
Citizen volunteer program coordinated through UF/IFAS Extension to monitor public water bodies across Florida.
Facilitates "hands-on" citizen participation in the management of Florida lakes, estuaries, rivers and springs through monthly monitoring activities.
Michigan CLMP
Website: https://www.micorps.net/lakes
The Cooperative Lakes Monitoring Program run via the Michigan Clean Water Corps and state universities.
Provides volunteers with a framework to monitor indicators of water quality.
Minnesota volunteer water monitoring
Website: https://www.pca.state.mn.us/get-engaged/volunteer-water-monitoring
Volunteers gather critically important water clarity data on Minnesota lakes and streams.
For some bodies of water, volunteer monitoring provides the only data available, making this work indispensable.
Wildlife Monitoring
eBird (Global)
Managed by the Cornell Lab of Ornithology.
Bird observations help scientists monitor migration, habitat use, and ecosystem changes.
Because birds are important hosts for some microbes and parasites (like the avian schistosomes that cause swimmer's itch), these data also have broader ecological value.
iNaturalist (Global)
Photograph and identify plants, fungi, insects, birds, amphibians—even algae and cyanobacteria.
Observations are verified by the community and contribute to biodiversity research.
In addition to those, many U.S. states now have Harmful Algal Bloom (HAB) reporting systems where members of the public can report suspected blooms. These reports often trigger follow-up investigations by state agencies. As of recording, the EPA website has links to all state HAB reporting systems but... I mean... there's no guarantee they won't remove it the way this admin is hobbling public health. So if it's ever gone, contact your local health department for info on where you can report an HAB.
Closing
By late morning, the towels are spread across the grass, drying in the sun, and the cooler is nearly empty. They're folding beach chairs and packing the car. Before leaving, someone turns back for one last look across the lake and says, "That water felt amazing."
And it did. Because for most of us, a morning at the lake isn't about microbes. It's about memories. The microbes were there, of course. They always are. Quietly photosynthesizing, recycling nutrients, feeding fish, supporting birds. Occasionally causing an itchy rash and very rarely, making someone sick. Most of the time, they're just helping sustain one of Earth's most remarkable ecosystems.
So enjoy the lake. Pay attention to changing conditions and respect the ecosystem you're stepping into, but enjoy it.
If you enjoyed today's episode, I'd love it if you'd share it with a friend or leave a review wherever you listen to podcasts. It really does help more people discover Infectious Dose.
And if you'd like to keep the conversation going, be sure to subscribe to my free weekly newsletter, Field Notes. Every Wednesday, I share the stories behind the science, highlights from the week's infectious disease news, and a few things that caught my attention along the way.
Thanks for spending part of your day with me—and thanks for being here.
Next week, our August series, From Sunrise to Starlight, continues as we trade towels for picnic blankets and explore the hidden infectious disease stories behind one of summer's favorite traditions.
Annotated Citations coming soon
Accessing the literature: Whenever possible, I've linked directly to free full-text articles and books that are legally available online. For subscription-only journal articles, many researchers are happy to share a personal copy of their work if you contact the corresponding author. For books, I've included links to free online lending copies or library catalogs when available. If a title isn't freely available online, I've linked WorldCat to locate it at a nearby library or you can ask your local library about interlibrary loans.
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