Monitoring Estuaries

Estuaries Tutorial

The National Estuarine Research Reserve System, or NERRS is a partnership program between NOAA and U.S. coastal states that protects more than one million acres of estuarine land and water. These estuarine reserves provide essential habitat for wildlife; offer educational opportunities for students, teachers and the public; and serve as living laboratories for scientists.

The health of every reserve is continuously monitored by the NERRS System-wide Monitoring Program or SWMP (pronounced “swamp”). SWMP measures changes in estuarine waters to record how human activities and natural events affect coastal habitats.

The instrument above is a YSI 6000 UPG Multi-Parameter Water Quality Monitor. This particular model measures dissolved oxygen, salinity, temperature, pH, depth, and turbidity.

The instrument above is a YSI 6000 UPG Multi-Parameter Water Quality Monitor. This particular model measures dissolved oxygen, salinity, temperature, pH, depth, and turbidity. (Photo Credit: Matt Ferner)

The NERRS SWMP uses automated data loggers to monitor the temperature, depth, salinity, dissolved oxygen, turbidity, and pH of each estuary’s water. These variables are recorded every 30 minutes at four stations in each of the 26 NERRS sites. They are key indicators of water quality and environmental conditions for the plants and animals that live in or use the estuary. The reserves also sample the water for nutrients (nitrogen and phosphorus) and chlorophyll on a monthly basis.

Weather can have a major impact on water quality in estuaries. For example, rainfall can increase sediment runoff, which, in turn, influences dissolved oxygen, turbidity, pH and temperature. As part of SWMP, every reserve has a weather station that collects data every 15 minutes on temperature, relative humidity, atmospheric pressure, rainfall, wind speed and direction. Several reserves are able to send real-time data as they are collected directly to Web sites on the internet.

These data have already helped scientists gain a better understanding of how environmental conditions fluctuate in estuaries. The SWMP data have been used to detect conditions related to oyster diseases, measure the recovery of estuaries after hurricanes, and evaluate restoration projects in estuaries.

Water Temperature

Just knowing the temperature of the water in an estuary can give us a pretty good idea of how healthy it is. One important thing we can tell from water temperature is how much oxygen can be dissolved into the water.

Dissolved oxygen is critical for the survival of animals and plants that live in the water. The more oxygen there is in the water, the healthier the ecosystem is. As the water temperature increases, the amount of oxygen that can dissolve in the water decreases. For example, fresh water at 0°C can contain up to 14.6 mg of oxygen per liter of water, but at 20°C, it can only hold 9.2 mg of oxygen per liter. Thus, seasonal water temperature (and dissolved oxygen) is an important indicator of habitat quality for many estuarine species.

The temperature of the water also tells us what types of plants and animals are able to live in the estuary. All plants and animals have a range of temperatures in which they thrive. If the water in the estuary is outside the normal seasonal temperature range in which most estuarine organisms can comfortably live, it is probably an indication that something is adversely affecting the health of the estuary.

This animation shows how increasing temperature affects the concentration of oxygen in water. When the animation starts, the temperature of the water cube is very low. At low temperatures the molecules move slowly, and a lot of oxygen can be dissolved into the water. As the animation progresses, the temperature of the water increases. With increasing temperature the molecules' movement increases, and most of the oxygen escapes into the atmosphere.


Water levels in an estuary typically rise and fall with the daily tides, but they are also affected by the weather. Periods of drought or excessive rainfall affect the amount of fresh water entering the estuary from rivers or runoff, and can easily change the physical, chemical and biological conditions in an estuary.

Depending on the source of pollution, the levels of toxins, bacteria, or nutrients may rise as runoff increases due to heavy rainfall. The concentration of dissolved and suspended materials in the water, or turbidity, may increase with runoff due to storms, or during periods of drought when there is a low volume of water in the estuary and winds and waves stir up the muddy bottom at low tide. In general, when water levels are too high or too low in an estuary for prolonged periods of time, the health of the estuary, and the plants and animals that live in it, are vulnerable to damage.

The NERRS SWMP uses electronic depth gauges to determine estuarine water levels throughout the year. To verify the accuracy of these sophisticated devices, researchers often go out and take measurements the old-fashioned way, by hand. (Photo: Hudson River NERRS site)

measuring water depth

The image above is the Mississippi Delta as viewed from space. The city of New Orleans is in the center left-hand side of the image. The massive deposits of sand and silt that make up the delta appear light tan in color, surrounding the peninsula. (Photo: Weeks Bay National Estuarine Research Reserve)


Under laboratory conditions, pure water contains only oxygen and hydrogen atoms, but in the real world, many substances are often dissolved in water, like salt. Salinity is the concentration of salt in water, usually measured in parts per thousand (ppt). The salinity of seawater in the open ocean is remarkably constant at about 35 ppt. Salinity in an estuary varies according to one's location in the estuary, the daily tides, and the volume of fresh water flowing into the estuary.

In estuaries, salinity levels are generally highest near the mouth of a river where the ocean water enters, and lowest upstream where freshwater flows in. Actual salinities vary throughout the tidal cycle, however. Salinity levels in estuaries typically decline in the spring when snowmelt and rain increase the freshwater flow from streams and groundwater. Salinity levels usually rise during the summer when higher temperatures increase levels of evaporation in the estuary.

Estuarine organisms have different tolerances and responses to salinity changes. Many bottom-dwelling animals, like oysters and crabs, can tolerate some change in salinity, but salinities outside an acceptable range will negatively affect their growth and reproduction, and ultimately, their survival.

Salinity also affects chemical conditions within the estuary, particularly levels of dissolved oxygen in the water. The amount of oxygen that can dissolve in water, or solubility, decreases as salinity increases. The solubility of oxygen in seawater is about 20 percent less than it is in fresh water at the same temperature.

freesh and salt ater mixing zones

The degree to which fresh water and saltwater mix in an estuary is measured using isohalines. Isohalines are areas in the water that have equal salt concentrations, or salinities. In estuaries, salinity levels are generally highest near the mouth of a river where the ocean water enters, and lowest upstream where fresh water flows in. To determine isohalines, scientists measure the water's salinity at various depths in different parts of the estuary. They record these salinity measurements as individual data points. Contour lines are drawn connecting data points that have the same salinity measurements. These contour lines showing the boundaries of areas of equal salinity, or isohalines, are then plotted onto a map of the estuary. The shape of the isohalines tells scientists about the type of water circulation in that estuary.

Dissolved Oxygen

To survive, fish, crabs, oysters and other aquatic animals must have sufficient levels of dissolved oxygen (DO) in the water. The amount of dissolved oxygen in an estuary’s water is the major factor that determines the type and abundance of organisms that can live there.

Oxygen enters the water through two natural processes: (1) diffusion from the atmosphere and (2) photosynthesis by aquatic plants. The mixing of surface waters by wind and waves increases the rate at which oxygen from the air can be dissolved or absorbed into the water.

DO levels are influenced by temperature and salinity. The solubility of oxygen, or its ability to dissolve in water, decreases as the water’s temperature and salinity increase. DO levels in an estuary also vary seasonally, with the lowest levels occurring during the late summer months when temperatures are highest.

Bacteria, fungi, and other decomposer organisms reduce DO levels in estuaries because they consume oxygen while breaking down organic matter.

Oxygen depletion may occur in estuaries when many plants die and decompose, or when wastewater with large amounts of organic material enters the estuary. In some estuaries, large nutrient inputs, typically from sewage, stimulate algal blooms. When the algae die, they begin to decompose. The process of decomposition depletes the surrounding water of oxygen and, in severe cases, leads to hypoxic (very low oxygen) conditions that kill aquatic animals. Shallow, well-mixed estuaries are less susceptible to this phenomenon because wave action and circulation patterns supply the waters with plentiful oxygen.


Low levels of dissolved oxygen in the water can cause marine life to become very lethargic. Along the eastern shore of Mobile Bay, Alabama, many aquatic animals move into shallow waters to try to get more oxygen. Local communities refer to this phenomenon as "Jubilee." During a Jubilee, residents walk along the shore and fill their ice chests with crabs and flounders. (Photo: Weeks Bay National Estuarine Research Reserve)


Turbidity is essentially a measurement of how cloudy or clear the water is, or, in other words, how easily light can be transmitted through it. As sediments and other suspended solids increase in the water, the amount of light that can pass through the water decreases. Thus, the cloudier the water, the greater the turbidity. As algae, sediments, or solid wastes increase in the water, so does turbidity.

Turbidity affects organisms that are directly dependent on light, like aquatic plants, because it limits their ability to carry out photosynthesis. This, in turn, affects other organisms that depend on these plants for food and oxygen.

Scientists often consider turbidity of the water in connection with other factors to get a better understanding of its causes and consequences. For example, high levels of turbidity can identify problems with shoreline erosion, or sewage processing facilities not functioning properly.

Click or tap on the video to play. Turbidity is measured at many NERRS sites using an electronic monitor. Another way to measure turbidity is to lower a device called a Secci (pronounced seh-key) Disc into the water. A Secci Disc has black-and-white elements. As the disc is lowered into the water, increasing turbidity will cause the black-and-white areas to fade into one another, and the disc will slowly disappear from sight. To determine the turbidity of the water, a mathematical calculation is performed based on the depth of water at which the Secci Disc “disappeared.”


pH is a measure of how acidic a solution is. The pH scale ranges from 0 to 14. Solutions with a pH of less than 7 are acidic, and those with a pH greater than 7 are basic (or alkaline). Distilled water is neutral and has a pH of 7.

Knowledge of pH is important because most aquatic organisms are adapted to live in solutions with a pH between 5.0 and 9.0. The pH in an estuary tends to remain constant because the chemical components in seawater resist large changes to pH. Biological activity, however, may significantly alter pH in an estuary.

Through a process called photosynthesis, plants remove carbon dioxide (CO2) from the water and expel oxygen (O2). Since CO2 becomes carbonic acid when it dissolves in water, the removal of CO2 results in a higher pH, and the water becomes more alkaline, or basic. When algae naturally begin to increase in estuaries during the spring, pH levels tend to rise. An overabundance of algae (called an algal bloom) may cause pH levels in an estuary to rise significantly, and this can be lethal to aquatic animals.

Click or tap on the video to play. This animation shows a parcel of water as its pH changes from acidic to alkaline. As the animation begins, the water appears red because it contains many hydrogen ions (H+), represented by red particles. As the animation progresses, the number of hydronium ions (-OH), represented by blue particles, increases. Soon they outnumber the hydrogen ions, and the water turns alkaline (blue in color).


Nutrients, especially nitrogen and phosphorus, are key indicators of water quality in estuaries. Plants require many nutrients (e.g., carbon, nitrogen, phosphorus, oxygen, silica, magnesium, potassium, calcium, iron, zinc, copper) to grow and reproduce. Of these, nitrogen and phosphorus are the most essential for aquatic plants.

Nitrogen and phosphorus naturally enter estuarine waters when freshwater runoff passes over geologic formations rich in phosphate or nitrate, or when decomposing organic matter and wildlife waste get flushed into rivers and streams. Manmade sources of nutrients entering estuaries include sewage treatment plants, leaky septic tanks, industrial wastewater, acid rain, and fertilizer runoff from agricultural, residential and urban areas. Too much nitrogen and phosphorus acts as a pollutant in the water. This leads to explosive blooms in algae that cloud the water and deplete it of the oxygen that is critical for aquatic animals. This is called eutrophication.

Excessive nutrient concentrations have been linked to hypoxic (very low oxygen) conditions in more than 50 percent of U.S. estuaries. Under the worst conditions, the waters of an estuary can become anoxic (having no oxygen). High nutrient concentrations have also been linked to algal blooms such as red and brown tides, some of which produce harmful toxins. Nutrients are also believed to cause the growth of the potentially toxic organism Pfiesteria. Red and brown algal tides and Pfiesteria have been linked to fish and shellfish kills, and may be harmful to human health.

nutrient rich marsh

The image illustrates what an estuary with a healthy input of nutrients looks like — lush and vibrant.


Chlorophyll is a green pigment in plants that turns light energy into food and allows plants to grow, and releases oxygen in a process called photosynthesis. The microscopic one-celled plants that float in healthy waters are called phytoplankton. By measuring the amount of chlorophyll in the water, scientists can determine the density of phytoplankton in an estuary, and the amount of primary productivity (the conversion of light energy into plant material) taking place as well.

Phytoplankton forms the base of the aquatic food web in an estuary. It is eaten by zooplankton (microscopic animals) and small fish, which, in turn, are eaten by larger creatures. The abundance of healthy animals in an estuary often depends on the amount of phytoplankton and primary productivity taking place.

Click or tap on the video to play. This animation represents what happens when the concentration of microscopic green algae, and therefore chlorophyll, increases in a body of water. As the amount of green algae in the water increases, the water turns greener in color. The increase in algae provides more food for the zooplankton, whose numbers and activity increase as well.