Water Quality Monitoring

Underwater sewer pipe. Photo © Grafner/iStock

In order to understand if wastewater pollution is impacting a particular environment or establish the source and extent of the problem, it is important for managers to establish baseline conditions and set up a monitoring program. Even the smallest sampling projects benefit from careful planning to identify the problem, define clear methods and quality assurance steps, and consider data processing and communication plans.

The key stages in a water quality program are:

  1. Define the problem. What potential wastewater impacts do you hope to identify? What data already exist, such as site-specific information about wastewater infrastructure?
  2. Conduct targeted water quality monitoring using processes that incorporate input from experts where possible (e.g., which sites to monitor, what indicators to focus on, how will data be collected).
  3. Develop and implement advanced studies to help trace pollution sources.
  4. Analyze and summarize data for communication to partners, decision-makers, and any other important stakeholders, keeping in mind what data are compelling to your audience.
  5. Use the information to guide a planning process or management action.

Enroll in our free, self-paced Wastewater Pollution Online Course to learn more about these key stages.


To detect changes in water quality related to wastewater, reef managers should consider measuring the following indicators:

Nitrogen and phosphorus, essential nutrients for plants and animals, are common indicators of nutrients. Sources of nitrogen include wastewater treatment plant discharges, runoff from fertilized lawns and croplands, cesspools and failing septic systems, runoff from animal manure and storage areas, and industrial discharges that contain corrosion inhibitors. Common measures of nitrogen and phosphorus include: Total Nitrogen (all organic and inorganic, dissolved and particulate forms of nitrogen found in a sample), ammonia, nitrates, nitrites, and Total Phosphorus (all forms of phosphorous).

Lastly, silicate is an important chemical measure that is a signature of groundwater. High silicates indicate freshwater sources. Silicate is usually measured at a lab along with nitrate and phosphate. These indicators can be measured by an autoanalyzer or a lab facility for ~$50 USD/sample.

Salinity can be measured cheaply using a refractometer, and temperature with a portable sensor. Salinity might be especially useful when identifying sites for long term monitoring.

Dissolved Oxygen (DO) is an important parameter in assessing water quality because of its influence on marine organisms.

Low DO can indicate an abundance of phytoplankton or bacteria that is consuming oxygen. DO is measured using a calibrated multi‐parameter water quality meter—or sonde—(costing ~$1,000-$15,000 USD).

Turbidity—a key test of water clarity that might be impacted by phytoplankton—is commonly assessed using a Secchi disk to measure the depth to which sunlight penetrates.

Other portable digital methods, such as a conductivity meter and turbidity meter enhance the ability to collect data in real time but require maintenance and calibration.

Fecal indicator bacteria (FIB) from human waste such as E. coli, Enterococcus, or C. perfringens can be used to identify wastewater. Simple field tests have been developed that test for FIB in water. One example is in the case of rural Tanzania where hydrogen sulfide tests were provided to 433 households, enabling them to monitor their own water sources and make informed choices about water safety and treatment. Unfortunately for marine managers, in coastal regions the concentration of bacteria is typically too low for these kinds of field tests and lab analysis is required to detect them.

Another option is to collect water samples and conduct FIB testing using a satellite lab (~$3,000 USD) or traditional lab and culturing method, such as the Enterolert test (IDEXX) used by Surfrider at a cost of about $11 USD/sample.

Chlorophyll a is the main green photosynthetic pigment found in all plants including phytoplanktonic algae and a proxy for planktonic primary producers. The concentration of chlorophyll a in coral reef waters is an indicator of the abundance and biomass of phytoplankton, which are the direct or indirect source of food for most marine animals. Low chlorophyll a levels suggest good water condition. However, it is the long‐term persistence of elevated levels that is a problem, so chlorophyll a should be monitored at least monthly to quantify seasonal changes in phytoplankton biomass. Chlorophyll a can be measured with filtration and lab equipment and if sent to a lab, costs ~$20 USD/sample.

These data can identify patterns and major changes if collected over many years. Managers can use this information to start to correlate water quality data/patterns with patterns of coral health and percent coral cover. These indicators are also relatively cost efficient. There are several field tests that can be performed with portable kits or relatively inexpensive (<$1,000 USD) handheld devices. These field tests require small volume water samples and provide results within minutes. For managers with limited time or budget to commit to a monitoring program, these are the first methods that can be used. Managers might consider what the detection limits are to these methods and if they are appropriate in their region. For instance, in clear ocean waters, it might be difficult to pick up a chlorophyll a signal or use a Secchi disk.

Tests to Detect Changes in Water Quality:

Chlorophyll aChlorophyll meter
DO (dissolved oxygen)Sensor measurement or calorimeter
Total Dissolved Solids (TDS) or TurbiditySecchi disk, turbidity meter, or sensors

It’s important to acknowledge these indicators don’t directly indicate wastewater pollution since other sources or factors can contribute to modified levels. For example, nutrients could be from agriculture or development and fecal indicator bacteria can also come from animals or soils.

Tracing Pollution Sources

Identifying the presence of wastewater in the ocean is difficult and relies on multiple tests to identify different contaminants commonly found in wastewater. More sophisticated testing that measures nitrogen isotopes and contaminants that have a human source like pharmaceuticals and organic-waste compounds, such as detergent metabolites or food additives, can help confirm wastewater and its source(s).

There are tests that can provide more specific measurements and identify contaminants more commonly associated with wastewater but they are often expensive to run because they require access to specialized, expensive machines and trained technicians.

Tests to Trace Pollution Sources:

CaffeineMass spectrometry
DNALab test (eDNA qPCR or fluorescence quantification)
PharmaceuticalsELISA, bioassays
Endocrine Disruptors (e.g., estrogen)Mass spectrometry, bioassays (exposure of fish or tissue cultures)
Bacteria (E. coli, E. faecalis, C. perfringens)Quantification measurement by heterotrophic plate count, microarray, or qPCR
MetalsMass spectrometry
Nitrogen IsotopesMass spectrometry
SterolsMass spectrometry
SucraloseMass spectrometry

Water samples are taken in the field and often require large volumes which must be concentrated to perform the analysis. If a lab is not nearby, samples can be shipped, but temperature, time, and cost are all limitations. It is recommended that managers work on creating collaborations or partnerships with local universities, who are often excited to have students working on real-life issues, and can help to offset the costs of sample analysis and data analysis with grant funding. Each water quality indicator contributes to our understanding of what pollutants are in our water. Monitoring and analysis strategies that compile measurements of several indicators, combined with mapping of discharge locations, can more accurately pinpoint wastewater pollution types and sources.

See the Resources section for more detailed water quality monitoring methodologies.


Examples of Monitoring Programs

  • Hui O Ka Wai Ola on Maui, Hawaiʻi is a water quality sampling program whose mission is to deepen the understanding of Maui’s coastal water quality through science and advocacy to accelerate positive change.
  • Volunteers collect water samples to track turbidity and nitrates using standardized EPA methods that are approved by the State of Hawaiʻi Department of Health. Samples and data are collected by volunteer citizen scientists and are used for decision making around water quality standards and management plans.
  • Data from field sampling efforts are consolidated into a database support ongoing monitoring that are used in analysis, to track pollution events, and to recognize water quality and coral reef trends over time.
  • The goal of the Surfrider Bluewater Task Force Program goal is to raise awareness about local pollution problems and bring together communities to implement solutions.
  • It includes 50 chapter-run labs and volunteers who test water quality at surfing beaches including those in Hawaiʻi, Florida, and Puerto Rico.
  • The water tests measure fecal indicator bacteria (Enterococcus bacteria, which is different from the Maui program which tests turbidity and nitrates) and test different sources of pollution (drainage pipes, etc.) and then are compared to water quality standards set by the EPA to protect public health in recreational waters.

Data for Monitoring Programs

Innovative and cost-effective measurement and reporting tools are needed to help marine managers uncover wastewater pollution issues and sources in less resource-intensive ways. Data including visualizations and modeling, remote sensing, and spatial imagery supplement wastewater pollution monitoring efforts and help inform management actions. Models created using local data can be particularly useful in predicting water quality.

Other tools collect global data on algal blooms, coral bleaching events, sea surface fluctuations, and eutrophication potential, which have local application and relevance. Publicly available data can be combined with local geographic data, such as locations of wastewater treatment plants, to understand pollution sources. Managers can also combine these data with field and lab tests to understand baseline conditions, prioritize monitoring tests, and identify data gaps to better quantify water quality changes over time. Examples of these online data platforms/visualization tools, include:

  • Ocean Tipping Points, which presents quantifiable measures of water quality (like nitrogen and phosphorus levels) with observed reef conditions in an interactive map. This tool provides a dataset for the Hawaiian Islands and supports management actions to protect reef ecosystems. It also includes a nutrient layer which was created using the InVEST NDR model, which looks broadly at nitrogen and phosphorus sources.
  • Allen Coral Atlas, which utilizes high-resolution satellite imagery and advanced analytics to map the world’s coral reefs in unprecedented detail. A new turbidity layer has been added, which could be helpful for water quality monitoring. These products support coral reef science, management, conservation, and policy across the planet.

How Monitoring Can Inform Wastewater Regulations

Regulations can aid in the mitigation of wastewater pollution for example by providing data on pollution thresholds. The establishment of local regulations to prevent wastewater-borne contaminants from reaching the threshold could then be implemented. With defined pollution thresholds, communities can better determine when specific responses should be taken, like shutting down beaches for recreation or issuing a boil water advisory. However, regulatory inconsistencies can present a complex challenge for wastewater managers making thresholds challenging to establish and enforce.

Several tools have been implemented by the US Environmental Protection Agency (EPA) to establish contaminant thresholds for water bodies and aquatic life. A commonly used threshold is a total maximum daily load, or TMDL, which limits the amount of a specific contaminant permitted to enter a water body. This is especially effective for wastewater contaminants that are derived from nonpoint sources. A few of the additional EPA tools include nutrient data layers (NPDAT), a water quality modeling program (WASP), and a diagnostic tool for biological impairment (CADDIS). These tools can help managers to identify and enforce wastewater pollution thresholds.

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