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Bacteria and Water: Tiny Organisms with a Big Impact

These tiny organisms can be found in all types of water and give us clues about water quality.

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Updated:

September 18, 2026

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A photograph of a wetland showing the rusty-orange slime color and oil sheen created by iron-eating bacteria. Travis Wingard - Penn State

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Water is full of life, including living things that are too small to see with the naked eye. Among the most common of these tiny organisms are bacteria. They can be found in rivers, lakes, streams, ponds, wetlands, groundwater, soil, and even inside our bodies.

Often, when people hear the word "bacteria," they think of diseases and stomachaches. However, most bacteria are not dangerous. Some bacteria are helpful and play important roles in nature and even in our bodies. Others act as indicators (clues) that help scientists find possible contamination (things we don't want) in water. Only a small number of bacteria can make people sick and affect human health.

What are "Bacteria"?

Bacteria are microscopic living organisms. There are many types of bacteria on Earth, and they can survive in a wide variety of environments. Individual bacteria are so small that they can only be seen with a microscope. In fact, the words microscope and microscopic come from the word parts micro (tiny) and scope (to look at).

Many bacteria are helpful. Some help break down dead plants and animals, returning nutrients to the environment. Others live in the digestive systems of people and animals, helping break down food. Without bacteria, dead leaves, fallen trees, and dead animals would remain in nature much longer than they do today.

Because bacteria occur naturally in the environment, finding bacteria in water is not unusual. The important question is not whether the bacteria are present, but which bacteria they are and what they can tell us about water quality.

How Do Bacteria Get into Water?

Bacteria can enter water in many, many different ways!

Some bacteria naturally occur in soil and surface waters and are carried wherever rainwater flows. Others come from wildlife, livestock, pets, or human activities.

Imagine a rainstorm moving across a neighborhood, farm, or forest. As rainwater flows across the land, it can pick up soil, leaves, animal waste (poop), and other materials. Along the way, bacteria may be carried along with those things into nearby waterways.

Heavy rainfall can increase this movement of bacteria through the environment. As rainwater flows across the land or soaks into the soil, it can carry bacteria into streams, ponds, groundwater (water found beneath the Earth's surface), and springs. Flooding can spread bacteria even farther by carrying water across fields, roads, and other areas that are normally dry. In some cases, floodwaters can also overwhelm wastewater systems or carry untreated wastewater (used water from homes, businesses, and other buildings) into nearby waterways, adding even more bacteria to the water.

Not all bacteria enter water through pollution and wastewater. Many bacteria naturally live in soil, streams, ponds, and wetlands. When scientists find bacteria in water, they are often more interested in understanding which bacteria are present, how they got there, and whether they might indicate a water quality problem.

Coliform Bacteria: Nature's Warning Sign

One of the most important groups of bacteria in water quality science is known as coliform bacteria. Coliform bacteria are commonly found in soil, plants, and the digestive systems of people and animals. Most coliform bacteria do not cause disease. Instead, scientists use them as indicator organisms because they can help show when contamination may be entering a water source.

A petri dish with black dots distributed throughout. — A round laboratory dish showing colorful spots where colonies of coliform bacteria are growing on a special gel. (Penn State Extension)

Think of coliform bacteria like a smoke alarm. A smoke alarm does not prove there is a fire; it alerts you to investigate further because something could be wrong. In the same way, finding coliform bacteria encourages us to ask more questions about the water, including whether it is healthy and safe and what may have gotten into it.

E. coli: A Stronger Signal

One type of coliform bacteria is called E. coli. It normally lives in the digestive systems of people and animals where it helps break down food. In the right place, E. coli can be helpful. When scientists find E. coli in our water, however, it can indicate that human or animal waste (poop) is present.

Pink rod shaped bacteria on a purple background as seen under a microscope. — A super-zoomed-in, colorized microscope photo showing a cluster of rod-shaped *E. coli* bacteria growing together (Janice Haney Carr/CDC Public Health Image Library)

Think of E. coli like seeing smoke after a smoke alarm goes off. While coliform bacteria suggest that contamination may be entering the water, E. coli provides even stronger evidence that human or animal waste has entered the water source. Although finding E. coli does not automatically mean someone will get sick, it does tell scientists that the water needs a much closer look. Some strains of E. coli can cause illness, including stomach cramps and diarrhea, which is why we commonly test for it in our drinking and recreational waters.

Water that appears clear can still contain bacteria. In a recent Pennsylvania State University study, researchers tested untreated roadside springs across Pennsylvania. Many of the springs contained coliform bacteria and E. coli, even though the water often looked clean and tasted good. Appearance alone cannot determine whether water is safe because it may contain bacteria and other contaminants that cannot be seen, smelled, or tasted.

Not All Water Bacteria are Dangerous

Not every bacterium found in water is a threat to human health!

For example, iron bacteria and sulfur bacteria occur naturally in some groundwater supplies. These bacteria use iron, manganese, or sulfur compounds to grow. As they reproduce, they can create slimy coatings, stains, unpleasant odors, and other nuisances.

Pink colored water in a wetland area indicates sulfur bacteria. — Purple sulfur bacteria turns the water pink at Keālia Pond National Wildlife Refuge in Maui, Hawaii (U.S. Fish & Wildlife Service)

Although these bacteria can be annoying and may affect the appearance, smell, or taste of water (I suggest not tasting orange swamp water because it's really gross), they are usually more unpleasant than dangerous. Like other bacteria, they are simply living organisms trying to survive and reproduce. The difference is that iron and sulfur bacteria get their energy from naturally occurring minerals in groundwater rather than from the digestive systems of people and animals.

So Why Do We Monitor Bacteria?

Bacteria are more than tiny organisms; they are also important clues that help us understand water quality. Different bacteria can help identify contamination sources, track changes, and indicate potential health concerns.

The information gathered from bacteria monitoring helps communities make decisions about drinking water and recreational waters. High bacteria levels may indicate a water quality problem and can lead to additional testing, boil-water advisories, or temporary closures of swimming and boating areas until the water is considered safe again.

Bacteria are a natural part of every aquatic ecosystem. Many are helpful, some are harmless, and a few can indicate contamination or cause illness. By understanding where bacteria come from and what they tell us about water quality, we can better protect rivers, lakes, ponds, groundwater, and drinking water supplies.

While these tiny organisms are too small to see with the naked eye, they play an important role in helping us understand and protect one of our most valuable natural resources: water.