On a hot summer day, few things are more inviting than diving into a cool lake. Natural bodies of water offer recreation, relaxation and a connection to the outdoors. But unlike chlorinated pools, lakes are not treated or disinfected, which means bacteria and other microorganisms can sometimes pose serious health risks.

Understanding what may be lurking beneath the surface can help you make safer choices before you jump in.

Why lakes can harbor harmful bacteria

Lakes are dynamic ecosystems influenced by rainfall, runoff, wildlife and human activity. Bacteria can enter the water from:

  • Stormwater runoff carrying animal waste
  • Failing septic systems
  • Agricultural runoff
  • Waterfowl and other wildlife
  • Warm temperatures that promote bacterial growth

When conditions are right, especially during hot weather, certain bacteria can multiply quickly.

Common bacterial threats in lakes

Here are some of the most common bacteria associated with freshwater swimming:

  • Escherichia coli (E. coli) is commonly found in the intestines of humans and animals. While many strains are harmless, high levels in lake water indicate fecal contamination. Some strains can cause:
    • Diarrhea
    • Stomach cramps
    • Nausea and vomiting

Elevated E. coli levels are one of the primary reasons beaches temporarily close.

  • Cyanobacteria (blue-green algae) are bacteria that can form harmful algal blooms (HABs). These blooms often appear as green, blue or reddish scum on the water’s surface. They can produce toxins that may cause:
    • Skin rashes
    • Eye irritation
    • Liver damage
    • Neurological symptoms, in severe cases

Children and pets are especially vulnerable because they are more likely to swallow lake water.

  • Vibrio bacteria are more commonly found in warm coastal waters but can occasionally appear in freshwater during hot weather. Certain strains can cause serious infections if they enter through cuts or scrapes.

Who is most at risk swimming in freshwater lakes?

While anyone can get sick from contaminated water, some groups are more vulnerable:

  • Young children
  • Older adults
  • Pregnant women
  • People with weakened immune systems
  • Individuals with open wounds

Swallowing even small amounts of contaminated water increases their risk of illness.

Warning signs to notice

Before swimming, look for:

  • Posted health advisories
  • Unusual discoloration of the water
  • Surface scum or foam
  • Strong odors
  • Dead fish or wildlife

After swimming, seek medical attention if you experience:

  • Persistent diarrhea
  • Fever
  • Severe headache
  • Rash that worsens
  • Redness or swelling around a wound

How to reduce your risk

You don’t have to avoid lakes entirely but take these precautions:

  • Check local water quality reports before visiting
  • Avoid swimming after a heavy rainfall
  • Don’t swallow lake water
  • Shower after swimming
  • Keep cuts covered with waterproof bandages
  • Avoid areas with visible algae blooms

If the water looks questionable, it’s best to stay out.

Key takeaways

  • Lakes can contain harmful bacteria from runoff, wildlife and warm temperatures, increasing health risks compared to treated pools. 

  • Common threats include E. coli (linked to fecal contamination), cyanobacteria (toxic algal blooms) and, less commonly, Vibrio bacteria. 

  • Higher-risk groups include children, older adults, pregnant women and those with weakened immune systems or open wounds. 

  • Stay safe by checking water conditions, not swallowing lake water and watching for warning signs like discoloration or algae.

Samir Desai, MD

Samir Desai, MD, is a board certified infectious disease specialist with KC Infectious Disease Consultants, LCC. 

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