Methods

Using existing data, APCC grades the following water resources:

• Coastal waters in tidal embayments or estuaries;
• Freshwater ponds and lakes; and
• Public water supplies for drinking water (i.e., drinking water after it is treated by the public water supplier and before it is distributed to consumers).

APCC uses three grading systems, one system for coastal waters, a second system for freshwater ponds and lakes, and a third system for public water supplies that provide drinking water. Each of the grading systems scores water quality parameters. The scores are then translated into a status category (i.e., acceptable or unacceptable for freshwater and saltwater surface waters, and excellent, good, or poor for drinking water supplies). APCC uses standardized grading systems that meet the following criteria:

• Are scientifically sound;
• Have been used before to evaluate water quality;
• Use key water quality parameters to evaluate water quality problems;
• Allow for annual updating using the most recent available data;
• Are easily understood and can be replicated by others; and
• Evaluates the most pressing water quality problems.

We update grades every year using a five-year rolling window—dropping the oldest year and adding the newest data available through the prior calendar year—to keep the assessment as current as possible.

In 2025, APCC migrated its coastal station and freshwater pond analyses from Microsoft Excel to the statistical programming language, R (Version 4.5.2). Instead of manual spreadsheet steps, R runs a scripted workflow that applies the same formulas every time and automatically produces the final outputs. You can review the programs on the State of the Waters Resources page. Although writing the scripts required upfront effort, they now process new data in minutes and improve efficiency, consistency, and reproducibility. Appendix A, available on the State of the Waters Resources page, provides results and explanation from the comparison of the previous Excel-based approach (“old”) against those from the new R workflow (“new”).

In addition to the development of the R program, in 2025 APCC partnered with the Cape Cod Commission to acquire exported water quality monitoring datasets from the Commission’s Cape Cod Water Quality Data Portal (hereafter referred to as the “CCWQ Portal”). We use exports from the CCWQ Portal for several reasons. Data ingested into the portal receives an additional quality-control review. Once uploaded, it can be exported in a standardized format, eliminating time-consuming spreadsheet reformatting and reducing the risk of errors. The portal also aggregates data across monitoring programs for each embayment or pond, increasing seasonal sample counts and site coverage—yielding a more comprehensive picture of conditions. Finally, by helping the Commission with annual portal updates, we lessen the burden on data providers to submit the same data to multiple organizations.

Advisory Committee: To help advise this project at its inception, APCC convened an Advisory Committee composed of experts in Cape Cod’s water pollution issues, nutrient issues, water monitoring, drinking water, aquatic ecosystems, fisheries, natural resource management and municipal management. Members of the following local, regional and state agencies, environmental nonprofit organizations and partnerships provided advice and guidance on the scoring systems described in the following sections: School for Marine and Atmospheric Sciences and Technology (SMAST); University of Massachusetts at Dartmouth; Cape Cod Commission; Center for Coastal Studies; Massachusetts Bays National Estuary Partnership; Massachusetts Office of Coastal Zone Management; Buzzards Bay Coalition; Marine Biological Laboratory, Woods Hole; Mashpee Water District; TMDL Solutions, LLC; Waquoit Bay National Estuarine Research Reserve (WBNERR); Department of Natural Resources, town of Chatham; and Department of Health and Environment, town of Eastham.

Grading Coastal Waters: Buzzards Bay Eutrophic Index

APCC uses an existing method of grading the severity of nitrogen pollution of coastal waters. The method is called the Buzzards Bay Eutrophic Index (aka “Bay Health Index”), developed in 1992 by the Buzzards Bay National Estuary Program. The Eutrophic Index was based on an earlier method developed by Hillsborough County, Florida, to evaluate coastal water quality.

The Buzzards Bay Eutrophic Index (EI) was developed to help the Buzzards Bay Coalition (BBC) evaluate citizen water quality monitoring data for Buzzards Bay embayments and to help rank each embayment with respect to its relative health for the purpose of prioritizing remedial management measures (i.e., Bay Health). The goal was to evaluate nitrogen loading inputs and to provide accurate and reliable water quality data for most of the major embayments around Buzzards Bay to assist environmental managers to:

• Establish baseline water quality;
• Characterize and identify sources of pollution;
• Document long-term environmental trends in water quality;
• Evaluate the relative success of cleanup efforts;
• Facilitate implementation of management efforts in the Comprehensive Conservation and Management Plan; and
• Evaluate the appropriateness of the Buzzards Bay Project’s recommended nitrogen limits.

The Eutrophic Index is considered by practitioners to be a well-tested method and is also used by the Center for Coastal Studies, the Pleasant Bay Alliance, and the town of Chatham to evaluate nitrogen pollution in coastal waters monitored by these organizations. The Eutrophic Index includes parameters that measure the degree of eutrophication: dissolved oxygen saturation, water clarity (measured using either Secchi disk or a turbidity meter), algal pigments, dissolved inorganic nitrogen (DIN), and total organic nitrogen (TON). Water quality data for these parameters are used to calculate a numerical score that indicates the degree of eutrophication.

The Dissolved Oxygen Saturation is a measure of the theoretical saturation of oxygen within the sampled water mass. All aerobic organisms (including finfish and shellfish) require oxygen to respirate, making this parameter an important indicator of habitat health.

Transparency, or water clarity, is the measure of light penetration in the water column. Light is an important driving force to plant and algal productivity, making it a key factor in habitat function. Transparency can be measured using two different methods: Secchi disk and turbidity.

Total Pigments is a combined measure of algal pigments, including chlorophyll-a and phaeophytin. Chlorophyll-a provides a proxy of phytoplankton biomass in the sampled water column. Phaeophytin is the measure of dead or dying phytoplankton cells, providing a more comprehensive understanding of recent algal productivity within a 24-hour period. Since phytoplankton species are sensitive to nutrient availability and concentrations are also driven by water flow and solar energy, this parameter is a helpful bioindicator of ecosystem health and function.

Dissolved Inorganic Nitrogen is the combination of bioavailable nitrogen compounds, nitrate-nitrite and ammonium; these are generally the first nitrogen parameters to be consumed by plants and algae. Because these compounds are rapidly taken up by primary producers, the concentration of these analytes is always low during the summer months.

Total Organic Nitrogen (TON) is the combination of dissolved organic nitrogen and particulate organic nitrogen (PON). PON consists of plankton, fragments from plants, algae, and animals, and suspended solids. High PON is a sign of excess nutrients and can lead to decreased water clarity and hypoxic (low oxygen) conditions.

Each parameter score is generated by averaging the summer measurements for each year and normalizing against a standardized range, or endpoints (Table 1). Stations located within or near a salt marsh receive adjusted endpoints to account for the greater exchange of nutrients and organic material intrinsic to these habitat types. Considerations that went into salt marsh designations include distance of salt marsh to the tidal inlet, size of salt marsh in relation to tidal sub-embayment (where salt marshes represented > 30-50% of the tidal pond area), proximity of station to the marsh, and size of sub-embayment opening to the rest of the estuary. Taken together, these considerations address the amount of time the sampled water mass is in direct contact with the salt marsh. In other words, water that has a high residence time (slow turnover) in a tidal pond that is in direct contact during the tidal cycle with salt marsh habitat received a salt marsh designation. Care was given to consider whether the station was upstream or downstream of the salt marsh during low tide, as samples are collected on an outgoing tide. The Coastal Embayment Master File, used to distinguish salt marsh stations for score calculations, is available on the Resources page.

Table 1: List of endpoints applied to normalize average annual measurements.

The Eutrophic Index (EI) score for each station is the average of the previous five years of combined parameter scores. In order to produce a final station score, the station must have at least three years of data, collected from June through September, within the five-year period. At least three of the five parameters (Dissolved Oxygen, Total Pigments, Transparency, Dissolved Organic Nitrogen, and Total Organic Nitrogen) must be measured within that specified timeframe and one of the three must be a nitrogen component.

State of the Waters Coastal Embayment Grading

APCC calculates numerical Eutrophic Index (EI) scores for coastal water quality from stations in coastal embayments and coastal waters around Cape Cod. However, APCC “grades” the numerical scores from individual stations in a manner that differs from the BBC. APCC assigns scores into two possible grades based on whether they indicate Acceptable water quality or Unacceptable water quality. The two grading categories were developed to indicate the type of action needed to protect or restore water quality (see below).

Grading coastal water quality at coastal stations:

EI scores greater than 65 (> 65) are graded as “Acceptable: requires ongoing protection.”

EI scores of 65 or below (? 65) are graded as “Unacceptable: requires immediate restoration.”

Waters that are graded as “Acceptable: requires ongoing protection” are waters that are healthy and free of excess nutrients. These waters need ongoing protection to remain healthy and free of pollution.

Waters that are graded as “Unacceptable: requires immediate restoration” are waters that are suffering from excess nutrients. These waters need immediate restoration in order to improve water quality.

Grading water quality in coastal embayments:

APCC has taken the additional step of identifying embayments where at least one monitoring station had Unacceptable water quality status—these embayments are considered “Unacceptable: requires immediate restoration.” Embayments where all monitoring stations had Acceptable water quality were graded as “Acceptable: requires ongoing protection.” This approach to grading embayments provides a clear indication of which embayments have portions with poor water quality that require restoration vs. embayments with good water quality that require protection.

Grading Freshwater Ponds and Lakes

To grade water quality in freshwater ponds and lakes, APCC uses two methods: (1) the Carlson Trophic State Index derived from water quality data, and (2) cyanobacteria grades based on APCC’s cyanobacteria monitoring data. The two methods are described below, followed by a description of how the two grading systems are combined into one grade per pond.

Method 1: Carlson Trophic State Index (TSI) scores

The first scoring method is the Carlson Trophic State Index (TSI) (Carlson, 1977), which evaluates the trophic state of the water body in terms of three important parameters for freshwater quality: total phosphorus, chlorophyll, and water transparency, or clarity.

Secchi Depth is a measure of water clarity, or transparency, and is measured using a Secchi disc. The disc is lowered into the water and the depth where the disc can no longer be seen by the sampler is recorded as the Secchi depth. 

Chlorophyll-a is an algal pigment necessary for photosynthesis and is used as a proxy for phytoplankton biomass (including cyanobacteria). High phytoplankton biomass is a symptom of excess nutrients in the pond. 

Total Phosphorus is an important measure of a freshwater pond’s limiting nutrient, meaning the concentration of phosphorus is the main driver in photosynthetic activity in the pond. When phosphorus is too high, there is an overload of plant and phytoplankton production which leads to low light levels, cyanobacteria blooms, and low oxygen conditions. 

The TSI was developed in 1996 to assess the trophic state of a freshwater pond or lake, where trophic state refers to the ecological response (in terms of algal or phytoplankton biomass) to nutrients. Since then, it has been widely used for evaluating freshwater ponds and lakes. Similar to the Buzzards Bay Eutrophic Index for coastal water quality, the TSI uses a numerical scoring system to evaluate pond trophic status. A eutrophic to hypereutrophic pond with high nutrient concentrations is characterized by high concentrations of algae, algal scums, poor water clarity due to dense algae, low to no dissolved oxygen, and TSI scores between 50 and 100. A mesotrophic pond with intermediate nutrient concentrations is characterized by moderately clear water, intermediate amounts of aquatic plants and algae, low dissolved oxygen during the summer, and TSI scores between 40 and 50. At the low end of the nutrient spectrum, an oligotrophic pond with low nutrient concentrations is characterized by clear well-oxygenated water, healthy aquatic plants, little to no algal growth, and TSI scores between 0 and 40.

APCC categorizes TSI scores into two possible grades for pond water quality:

TSI scores of less than 50 (< 50) are graded as “Acceptable: requires ongoing protection.”

TSI scores of 50 or above (? 50) are graded as “Unacceptable: requires immediate restoration.”

Ponds that are graded as “Acceptable: requires ongoing protection” are ponds that are healthy and free of excess nutrients. These ponds need ongoing protection to maintain healthy ecosystem function.

Ponds that are graded as “Unacceptable: requires immediate restoration” are ponds that are suffering from excess nutrients. These ponds need immediate restoration in order to improve water quality.

Data quality needed for TSI scoring: To provide a rolling view of recent conditions, each TSI analysis uses data from at least three of the past five years. Sites must also have measurements for all three TSI parameters—chlorophyll-a, total phosphorus, and water clarity (Secchi depth or turbidity)—to be included. As of 2025, only 76 ponds met these criteria, out of roughly 890 on Cape Cod, underscoring a significant gap in recent, Cape-wide pond monitoring needed to guide management and protection.

Method 2: Cyanobacteria Grades Using Cyanobacteria Monitoring Data

Since 2018, APCC has monitored cyanobacteria and cyanobacteria bloom activity in over 100 freshwater ponds across Cape Cod. Blooms occur when nutrients—especially phosphorus—are sufficient to fuel growth, with warm temperatures and sunlight further promoting proliferation. Where nutrients are scarce, cyanobacteria growth is generally limited (Merel et al., 2013). Because of this nutrient dependence, cyanobacteria blooms are a practical indicator of nutrient enrichment in freshwater ponds.

In 2024, APCC’s Cyanobacteria Monitoring Program finalized the Cape Cod Cyanobacteria Monitoring Program Quality Assurance Project Plan (CCCMP QAPP), which was approved by the EPA and MassDEP in July 2024. Prior to 2024, the Cyanobacteria Monitoring Program used an EPA-approved protocol developed by EPA for the Cyanobacteria Monitoring Collaborative and refinements added under the guidance of Dr. James Haney (emeritus professor, University of New Hampshire) and Nancy Leland of Lim-tex, Inc. (Leland and Haney, 2018; Leland, Haney, Conte, Malkus-Benjamin and Horseley, 2019). APCC’s CCCMP QAPP follows the methods described in the EPA-approved protocol, ensuring consistent sampling and analysis methods over time.

Data collected from ponds includes photographs and field observations, microscopy to identify composition and dominance of cyanobacteria genera, and concentrations of phycocyanin and chlorophyll pigments indicative of the biomass of cyanobacteria vs. biomass of other algae and phytoplankton, respectively. By monitoring biweekly/monthly from May to October, APCC tracks changes in cyanobacterial composition, dominance, and abundance throughout the season. The monitoring data are translated into three risk levels, which are reported to public health officials and the public to raise awareness of potential risks and to assist public health officials by providing credible monitoring data to inform proactive management actions to protect public safety. To learn more, visit APCC’s Cyanobacteria Monitoring Program.

The scarcity of recent pond water quality data needed to calculate TSI scores led APCC to adopt a second method of grading ponds in 2020 using cyanobacteria monitoring data to provide an additional measure of pond health. The use of cyanobacteria data helps to fill the gap in water quality data by providing a different measure of trophic status that relates directly to cyanobacteria biomass. APCC’s cyanobacteria grading system utilizes our three-tiered risk warning system for assigning monitored cyanobacteria concentrations into “Low,” “Moderate” and “High” risk tiers, which describe potential risks in terms of exposure to children, pets, exposure during recreational activities, toxin concentrations, and presence of visible cyanobacteria blooms. To grade ponds using cyanobacteria risk tiers, the tiers are assigned into “Acceptable” or “Unacceptable” grades according to the risk definitions. The previous year’s monitoring results are used (i.e., for this report, cyanobacteria data collected in 2023 were used). The highest risk tier documented in a pond during the monitoring season is used to assign a grade.

Cyanobacteria risk tiers and grading system:

APCC used the same cyanobacteria risk tiers as in the last three years of the State of the Waters: Cape Cod report (2022-2024). These risk tiers were adopted in 2022 for APCC’s Cyanobacteria Monitoring Program. The risk tiers reflect input from local and state public health officials and scientists, incorporation of state limits for cyanobacteria toxin in recreational waters, and a new regional capability for cyanobacteria toxin testing at the Barnstable County water quality lab. The risk tiers applied to the data collected in 2024 are given below. Note: The current APCC website has our most up to date 2025 risk tiers which differ slightly.

Acceptable (“Low” risk): No concerning cyanobacteria results at the time and place of sampling. To the best of APCC’s knowledge and based on our monitoring results, regular recreational usage of the pond is safe with respect to cyanobacteria and toxins. Map color is blue.

Potential for Concern (“Moderate” risk): Monitoring results or the presence of cyanobacteria scum at the time and place of sampling indicate a potential for increased risk for exposure to cyanobacteria toxins approaching, but below, state standards. Conditions do not yet warrant the posting of a recreational human health advisory according to guidelines from the Massachusetts Department of Public Health (MDPH). While these conditions pose low health risks to adults, risks are higher for children or pets based on lower body mass, particularly if contaminated water is incidentally ingested. Children may inadvertently consume pond water while swimming and pet exposure can result from drinking or ingesting pond water or from grooming after swimming. Map color is yellow. Map color yellow with crosshatching indicates a municipal pet advisory has been issued.

Use Restriction Warranted (“High” risk): Monitoring results at the time and place of sampling indicate the pond is unsafe for recreation by humans and pets based on one or more of the following criteria: 1) presence of microcystin at or above state standards (8 parts per billion or ppb microcystin) as described in MDPH guidance; 2) presence of significant cyanobacteria scum layers according to MDPH guidance; 3) a municipal health agent issues a closure for any other reason related to cyanobacteria. Recreational risk to adults is moderate following exposure. Recreational risks are especially high for children and pets following exposure through accidental ingestion of contaminated water. Children may inadvertently consume pond water while swimming and pet exposure can result from ingestion or directly drinking pond water or from grooming after swimming. Due to lower body masses, children and pets are more susceptible to cyanobacteria risks than adults. Map color is red. Map color red with crosshatching indicates a municipal advisory has been issued.

The cyanobacteria grading system is provided below:

If all cyanobacteria levels for the entire sampling season were in the “Low” and/or “Moderate” risk tiers, the pond was graded as “Acceptable: ongoing protection is needed”; and

If one or more of the cyanobacteria levels were in the “High” risk tier, the pond was graded as “Unacceptable: requires immediate restoration.”

Combined Pond Grading System

As in previous years, APCC’s combined pond grading system utilizes available Carlson Trophic State Index grades and cyanobacteria grades, as follows:

1. Trophic State Index (TSI) scores and grades were calculated only for ponds with water quality data collected within at least three of the past five years and where all three TSI parameters were available: chlorophyll-a, total phosphorus, and Secchi depth.
2. Cyanobacteria monitoring data from the previous year were used to grade ponds using APCC’s cyanobacteria risk tiers and grading system described above:
       a. Ponds with cyanobacteria levels in the “High” risk tier were graded as “Unacceptable: requires immediate restoration.”
       b. Ponds with cyanobacteria levels in the “Low” and “Moderate” risk tiers were graded as “Acceptable: requires ongoing protection.”
3. If a pond had both Trophic State Index grades and Cyanobacteria grades:
       a. The pond was graded as “Acceptable: requires ongoing protection” only if both grades were Acceptable.
       b. The pond was graded as “Unacceptable: requires immediate restoration” if at least one of the grades was Unacceptable.
4. If a pond had only one grade (i.e., Trophic State Index grade or Cyanobacteria grade), that grade was used as the sole determinant of the overall pond grade.

Grading Public Water Supplies of Drinking Water

The grading system for public drinking water supplies (PWSs) is based on a modification of a method developed by the Natural Resources Defense Council (NRDC) to grade drinking water. The NRDC grading system evaluates three areas of drinking water: water quality and compliance, source water protection, and right-to-know compliance. APCC evaluates water quality and compliance of public water supplies after treatment and before distribution to consumers, the so-called “finish water.” This represents the underlying quality of the public water supply before it is distributed to customers and consumers, not the quality of the water as it comes out of the tap, which can be affected by pipes and plumbing in the distribution system and in homes and businesses. APCC evaluates public water supplies in this manner because underlying water quality represents the first line of defense in ensuring safe drinking water supplies and because many water protection measures are aimed at protecting source water quality.

To grade Cape Cod public water supplies, APCC uses publicly available Consumer Confidence Reports (CCRs) for the previous year to determine if water quality met existing state and federal drinking water standards (i.e., Maximum Contaminant Levels, or MCLs). This year, 2023 CCRs were reviewed for grading.

The grading system used this year is the same as that used last year, i.e., a three-level grading system: “Excellent,” “Good,” and “Poor.” These are described below:

Excellent: Finish water met all existing state and federal health and reporting standards.

Good: Finish water had one or more exceedances of the Total Coliform MCL and/or no more than one violation of an existing state or federal standard that posed a risk to public health, and that violation was neither chronic nor repeated.

Poor: Finish water had violations of two or more existing state and/or federal standards that posed a risk to public health or a violation that was repeated or persisted through more than one sampling round.

In addition, APCC identified PWSs that had detectable PFAS6 but met the state standard with an asterisk (*). In April 2021, the new Massachusetts drinking water standard for PFAS6 went into effect (MassDEP PFAS Drinking Water Regulation Quick Reference Guide). PFAS refers to per- and polyfluoroalkyl substances, a family of manmade chemicals used in industry and consumer products worldwide since the 1950s to manufacture stain-resistant, water-resistant, and non-stick products. Thousands of PFAS compounds are known. PFAS6 refers to the sum of six per- and polyfluoroalkyl substances. The state’s PFAS6 standard is 20 parts per trillion (ppt) based on the average of the monthly samples over a quarter. If any single sampling location is in violation, then the PWS is in violation. If any sample result would cause the quarterly average to exceed the PFAS6 MCL, the PWS is immediately in violation and begins compliance actions.

Sources of Data

Collaboration with partners is an essential feature of State of the Waters: Cape Cod, involving the culmination of water quality monitoring efforts from many organizations. Cape Cod is fortunate to have many environmental organizations and agencies that have monitored water quality for many years. Over the years, hundreds of citizen scientists, local, state and federal government agencies, scientists, environmental organizations, consulting firms, and APCC interns and volunteers have collected water samples for different water quality monitoring programs. Go to the Cape Cod Commission’s Cape Cod Water Quality Data Portal to explore the monitoring programs that contributed to the data incorporated in the coastal and freshwater results.

The monitoring programs that contributed to the data results are provided on the Commission’s portal, however the funding sources of those monitoring efforts are not readily available. The following is a list of towns that contract the UMASS Dartmouth School for Marine Science and Technology (SMAST) to monitor their coastal embayments and/or freshwater ponds (freshwater ponds are considered part of the Ponds and Lakes Stewards, PALS, program):

• Town of Barnstable: coastal and pond water quality data;
• Town of Brewster: pond water quality data for one freshwater pond;
• Town of Chatham and Pleasant Bay Alliance: coastal water quality data;
• Town of Dennis: coastal water quality data;
• Town of Eastham: coastal and pond water quality data;
• Town of Falmouth: coastal and pond water quality data;
• Town of Harwich: coastal and pond water quality data;
• Town of Mashpee: coastal and pond water quality data; and
• Town of Orleans: coastal and pond water quality data.

Regional data sources. These sources provided data covering multiple embayments or large areas of the Cape:

• Association to Preserve Cape Cod: 2023 cyanobacteria monitoring data for freshwater ponds located in the towns of Barnstable, Bourne, Brewster, Chatham, Dennis, Eastham, Falmouth, Harwich, Mashpee, Orleans, Provincetown, Sandwich, Truro, Wellfleet, and Yarmouth;
      – Partners who assisted APCC with cyanobacteria monitoring included Brewster Ponds Coalition, Falmouth Water Stewards, Friends of Chatham Waterways, Friends of Long Pond Marstons Mills, Orleans Ponds Coalition, Oyster Pond Environmental Trust, the towns listed above, and other organizations and individuals; 
• Barnstable Clean Water Coalition: coastal water quality data for stations located in the Three Bays embayment and pond water quality data;
• Buzzards Bay Coalition: Eutrophic Index scores for coastal stations and embayments located along the coasts of Falmouth and Bourne in Buzzards Bay;
• Center for Coastal Studies: pond water quality data and coastal water quality data for stations located in embayments on Cape Cod Bay, Nantucket Sound and Vineyard Sound;
• Cape Cod Commission: coastal and pond water quality data collected by and for the Cape Cod Regional Water Quality Database, a project to collect and make publicly available all water quality monitoring data for the Cape. The project was funded by the EPA Southeast New England Coastal Watershed Restoration Program (EPA SNEP);
• Pleasant Bay Alliance: Eutrophic Index scores for stations located in Pleasant Bay; and
• Waquoit Bay National Estuarine Research Reserve (WBNERR): coastal water quality data for stations located in Waquoit Bay.