Water Quality Monitoring

Pipe Steve Spring Marine Photobank

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 exists, such as site-specific information about wastewater infrastructure?
  2. Conduct targeted water quality monitoring for water quality 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 opens in a new windowWastewater 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 per 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 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 (<$1000 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.

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 signify 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.

Trace 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). Enroll in the opens in a new windowWastewater Pollution Online Course to learn more about how different types of chemical tracers can be used to better understand where high concentrations of nutrients are coming from.

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

maui water quality

Poor water quality off the coast of Maui. Photo © Bill Rathfon for Hui O Ka Wai Ola (Association Of The Living Waters), a partnership of The Nature Conservancy

opens in a new windowHui O Ka Wai Ola

Hui O Ka Wai Ola is a citizen science water quality sampling program aligned with Hawai‘i Department of Health, Clean Water Branch standards and protocols. Samples and data collected are used for decision making around water quality standards and management plans. Samples collected in the field are brought to a local high school lab dedicated to water quality monitoring procedures. 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.

This program acknowledges the limitations any one water quality indicator may present. Each water quality indicator contributes to understanding, but no single measurement is sufficiently conclusive. Therefore, strategies that compile measurements of several indicators are more valuable. ref  This is especially important because of the lack of global agreement on pollution thresholds. For instance, enterococcus is the most commonly measured fecal indicator bacteria (FIB) in marine environments used to determine beach closures and advisories. However, another bacteria found in sewage, Clostridium perfringens, is considered a more accurate indicator of sewage pollution in Hawai‘i but is not approved for use nationwide. ref The lack of coordinated understanding of the ocean’s resilience to sewage pollution, as it impacts both marine and human health, necessitates establishing localized baselines and monitoring efforts for effective protection. For more information on this program view the webinar about Hui O Ka Wai Ola.

Resources and Tools for Monitoring Programs

Data visualization and modeling, remote sensing, and spatial imagery efforts supplement wastewater pollution monitoring efforts and help inform management actions. Models created using local data can predict 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. These opens in a new windowpublicly 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.

  • opens in a new windowHeal the Bay’s NowCast Beach Report Card, is a model to predict beach water quality in California, USA, and improves public awareness of contamination events.
  • Ocean Tipping Points 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.
  • Ocean Health Index presents global ocean health scores based on threats and resilience. A data layer specific to ocean wastewater pollution is in development and will be useful for data analysis and evaluations of the impacts of wastewater pollution.
  • Allen Coral Atlas utilizes high-resolution satellite imagery and advanced analytics to map the world’s coral reefs in unprecedented detail. These products support coral reef science, management, conservation, and policy across the planet. (NOAA Coral Reef Watch’s sea surface temperature products are included in the Atlas.)
water quality field measurements

Water quality field measurements by Hui O Ka Wai Ola citizen scientists. Photo © Bill Rathfon

There remains a need for innovative and cost effective measurement and reporting tools to identify sewage pollution. The opens in a new window Ocean Health Index is a project undertaken by NCEAS that presents ocean health scores based on threats and resilience. A data layer specific to sewage pollution in the ocean is in development and will be useful for data analysis and multi-scalar evaluations of the impacts of sewage pollution.

Bubbling sewage effluent Bubbling sewage effluent. Photo © Matthew Chatfield</

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