Clean water is central to the health of the Cape’s natural ecosystems. Our coastal waters, estuaries and embayments support valuable shellfish such as oysters and clams, as well as important finfish such as winter flounder and striped bass. Waterbirds, migrating waterfowl, raptors and wildlife feed on fish, shellfish and aquatic plants. Freshwater ponds and streams support numerous fish and wildlife species, including important diadromous species such as river herring and American eels, which live in both fresh water and the ocean. The Cape’s ecosystems and food webs depend upon clean water.

Clean water is also important for our economy. The Cape’s economy is a “blue economy” where our residents, visitors and businesses rely upon clean water and healthy natural resources. The economic benefits of clean water and healthy ecosystems are demonstrated by the fact that coastal tourism and commercial and recreational fishing and shellfishing and their supporting industries bring in more than $1 billion to the local economy. For example, in 2018 tourists visiting Cape Cod spent $1.32 billion that supported 10,844 tourism-related jobs and $357.7 million in wages, and generated $133 million in state and local taxes (Cape Cod Chamber of Commerce).

Commercial and recreational fishing and shellfishing also bring in additional millions of dollars each year. For example, from 2000 – 2004, the average annual value of commercial and recreational shellfishing was $11.4 million. In 2009 alone the value of commercial fishing was $19 million, while the value of commercial fishing for species that eat river herring was over $37 million (NRCS, Cape Cod Water Resources Restoration Project: Why It Matters to Massachusetts Economy). These numbers do not include water-focused organizations such as oceanographic institutions and businesses, non-governmental organizations, educational institutions and laboratories that employ people and provide services and products.

Finally, clean drinking water is critically important for human health. The water we drink comes from Cape Cod’s sole-source aquifer, a vast underground natural reservoir of groundwater. Federal, state and local laws are designed to protect a sole-source aquifer from pollution. However, as we discuss below, our groundwater, ponds, lakes, estuaries and embayments are all interconnected.


Cape Cod enjoys a wealth of water resources. These include salt water and freshwater resources. Each major resource is summarized below. More information can be obtained at the Cape Cod Commission’s website on water resources.

Coastal waters (saltwater) surround most of the Cape, creating over 559 miles of coastline bordering the Atlantic Ocean, Nantucket Sound, Vineyard Sound, Buzzards Bay and Cape Cod Bay. This long coastline contains 53 distinct saltwater embayments, places where there is a recess or indentation in the coastline that forms a bay bordering the ocean. Estuaries are places where rivers meet the sea. Estuaries typically contain a range of wetlands including freshwater, brackish and tidal wetlands (aka salt marshes) and tidal channels. On Cape Cod, rivers, streams and groundwater flow into estuaries and embayments that border the ocean.

Freshwater ponds and lakes: Few people know that the Cape is the land of nearly a thousand lakes. At least 890 freshwater ponds and lakes cover nearly 11,000 acres, and individual ponds and lakes range in area from less than one acre to 735 acres and include 166 “great ponds” of 10 acres or greater in size. Because the Cape’s ponds and lakes are fed by groundwater, they are often referred to as “windows on our aquifer.” The sandy soils of the Cape allow groundwater to flow into and out of ponds. For this reason, pollution of ponds will likely also pollute groundwater and vice versa.

Groundwater: Groundwater is the lifeblood of the Cape. Rain and melting snow quickly soak into our sandy soils where it collects to form a huge underground reservoir of groundwater that lies beneath most of the Cape. Water seeks the lowest elevation, so groundwater continues to move, seeking sea level, flowing into and out of ponds, feeding streams and flowing towards the coast, finding sea level when it enters our estuaries and embayments.

Groundwater is also the source of our drinking water. In 1982, the U.S. Environmental Protection Agency designated Cape Cod’s groundwater as a sole-source aquifer for drinking water under the federal Clean Water Act and Safe Drinking Water Act. All of the Cape’s drinking water comes from this sole-source aquifer, which is protected by local, regional, state and federal regulations. Nearly all of the Cape’s public water supplies are from groundwater wells, with one exception being Long Pond in Falmouth which is itself groundwater-fed.

Watersheds connect our waters: Nearly all of the Cape’s waters are connected by watersheds that collect water and discharge it into the ocean. Watersheds are the land areas that collect rain and snow, which drains into ponds, lakes, streams and groundwater, which in turn discharge into estuaries, embayments and the ocean. Cape Cod has a total of 101 watersheds that discharge to the ocean. Of these, 53 discharge to embayments, which are susceptible to nitrogen pollution, and the remainder discharge directly to the ocean. Through the Section 208 Water Quality Management Plan for Cape Cod, the Cape Cod Commission has created a regional blueprint for protecting and improving water quality and tracks progress in implementation.

Hydrological cycle: The Cape receives about 45 inches per year of rain and melting snow. About 60 percent of this precipitation soaks into the ground to replenish groundwater. Most of the remaining 40 percent evaporates into the atmosphere where it provides moisture for storms that provide rain and snow (see below). A small amount becomes stormwater runoff. Due to the sandy soils, this runoff generally soaks into the sand and replenishes the aquifer. However, when runoff flows from roads, parking areas and fertilized lawns directly into wetlands, ponds or the ocean, pollutants from these developed areas can enter the water. Stormwater pollutants can include fertilizers, bacteria, soil particles, metals and de-icing compounds.

Groundwater is used up (depleted) when we withdraw it for drinking water and when it flows into ponds, streams, embayments and into the ocean. Ponds, streams and wetlands lose water due to evaporation, and trees also “breathe” water back into the air in a process called “evapotranspiration.” This evaporated water is not truly “lost.” Instead, it is critically important for feeding water back into the atmosphere to grow storms that produce rain and snow. Groundwater is replenished by rain and melting snow, which soak into the ground, beginning the hydrological cycle all over again.


Most of the Cape’s coastal embayments and many freshwater ponds and lakes are suffering from water pollution, based on years of studies and reports on water quality and water pollution. These studies and reports indicate that the Cape’s waters suffer from pollution due to the following pollutants and pollution sources.

Nutrient pollution: Excess nutrients (nitrogen in coastal waters and phosphorus in fresh water) have caused severe eutrophication and severe ecological damage. Eutrophication refers to the harmful effects of excess nutrients on an aquatic ecosystem, resulting in increased growth of phytoplankton and depletion of oxygen. Excess nutrients in water stimulates the growth of phytoplankton (microscopic algae), which depletes the water of oxygen. Oxygen depletion leads to fish kills and impacts on shellfish and other aquatic life. Excess phytoplankton also causes water to become cloudy, reducing the amount of light in the water column, which impacts the growth of other beneficial aquatic plants such as eelgrass. When algae die, their remains settle to the bottom and decompose, causing more oxygen depletion and releasing nutrients back into the water, feeding the nutrient cycle. Also, the buildup of decaying organic matter on the bottom of ponds, lakes and embayments often results in thick muck that is unhealthy for shellfish, fish and other aquatic organisms.

Many of the Cape’s estuaries and embayments are suffering from eutrophication caused by excess nitrogen, as demonstrated by the Massachusetts Estuaries Project and by the Section 208 Water Quality Management Plan for Cape Cod.

Ponds and lakes are also suffering from eutrophication caused by excess phosphorus (Cape Cod Commission, Ponds and Lakes).

On Cape Cod, excess nutrients originate largely from human sources and activities. Excess nitrogen comes from poorly treated wastewater (e.g., Title 5 septic systems) as well as fertilizers used on lawns, gardens, golf courses and farms. Some nitrogen also falls out from the atmosphere in precipitation, and this atmospheric nitrogen largely originates from burning fossil fuels. Excess phosphorus comes from septic systems that discharge phosphorus into groundwater that enters ponds and lakes, as well as fertilizers used on lawns, gardens, golf courses and farms that is carried into ponds and lakes in stormwater runoff.

Harmful bacteria include bacteria that originate from fecal wastes (humans and/or animals). Examples of fecal bacteria are Escherichia coli (E. coli) and enteric bacteria. Fecal bacteria can cause illness in both humans and animals. On Cape Cod, most fecal bacteria contamination originates from domestic animals and wildlife. Failed septic systems (including flooded septic systems) are another source of bacteria. Bacteria are carried into water by stormwater runoff. State and federal water quality standards limit the amounts of fecal bacteria that can be present in waters where swimming and shellfishing are conducted. Swimming beach water quality is monitored by Barnstable County. The Massachusetts Division of Marine Fisheries monitors water quality in shellfish beds and limits shellfishing to waters that meet a stringent water quality standard for fecal bacteria.

Harmful algal and cyanobacteria blooms include toxic red tides in coastal waters and toxic cyanobacteria blooms in freshwater ponds and lakes. In coastal waters red tide is the common name for several species of toxic phytoplankton, including toxic dinoflagellates. Shellfish that ingest such toxic phytoplankton become toxic themselves, posing a threat to humans who eat contaminated shellfish and impacting the shellfishing industry. In fresh water harmful cyanobacteria that produce toxins thrive in nutrient-rich and warm waters. APCC’s Cyanobacteria Monitoring Program has documented cyanobacteria blooms in dozens of ponds throughout the Cape and we anticipate that this will be an increasing problem as nutrient pollution continues and the climate warms. This year is the second year that APCC has incorporated cyanobacteria monitoring data into our grading system for freshwater ponds as another indicator of nutrient pollution.

Mercury pollution occurs in waters throughout the Northeast. As of October 2021 the Massachusetts Department of Public Health listed 32 ponds and lakes on Cape Cod with fish consumption advisories that warn people (i.e., children under 12, pregnant women, nursing mothers, women of childbearing age, and the general public) to limit or avoid eating fish from that lake due to mercury pollution (MA DPH Fish Consumption Advisories). Mercury pollution is caused by fallout of mercury from the atmosphere, which originates from coal-burning fuel plant emissions. Incineration of medical wastes and municipal wastes also contributes mercury to the atmosphere. Our assessment does not address mercury pollution, but the State of the Waters; Cape Cod website provides information on mercury pollution and state fish consumption advisories for freshwater lakes and ponds on Cape Cod.

Emerging contaminants and pharmaceutical compounds have been found both in groundwater and surface water throughout Cape Cod. This group of pollutants contains a wide variety of compounds, including endocrine-disrupting compounds, pharmaceutical drugs (including antibiotics), insect repellant, flame retardant, fluorinated compounds and PFAS (per- and polyfluoroacetate substances). The Silent Spring Institute has been monitoring the Cape’s waters emerging contaminants. The Center for Coastal Studies and Silent Spring Institute also found pharmaceutical compounds in Cape Cod Bay and in groundwater near septic systems, pointing to septic systems as the source of these pharmaceutical compounds.

PFAS (per- and polyfluoroacetate substances) are manmade chemicals used widely in diverse items (e.g., fireproof clothing, non-stick pans, stain-and-waterproof fabrics, fire-fighting foam, dental floss, cleaning products, paints, electronics manufacturing and other industries and household products). PFAS are long-lasting compounds that have been found worldwide in humans, wildlife, water, soil and the air. PFAS have been found in Cape Cod water supplies, groundwater, and ponds (five of the ponds which have fish consumption advisories due to mercury also have fish consumption advisories due to PFAS). PFAS have been linked to human health impacts such as developmental disorders, immune system disorders, thyroid hormone disruption and cancer. Information on PFAS is provided in our PFAS Primer. In our next report in 2022, PFAS will be addressed in our drinking water grades for 2021. PFAS was not a scoring factor in this year’s report because state drinking water regulations for monitoring and reporting on PFAS did not become effective until January 2021.

Aeriel photo of Cape Cod pond

photo by Steven Koppel


To help people understand where water quality is acceptable vs. unacceptable, APCC has created this State of the Waters: Cape Cod project and website to collect existing information on water quality and translate it into easily understood terms by grading water quality. This website is a key means of collecting and distributing information to the public. Our intent is to guide public policy and investment in restoration and protection efforts.


Using existing data, APCC graded the following water resources:

  • Coastal waters in embayments and 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 used three grading systems, one system for grading coastal waters, a second system for grading ponds and lakes, and a third system for grading drinking water. Each of the grading systems scores water quality parameters. The scores were then translated into grades. APCC chose 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;
  • Are easily understood and can be replicated by others (e.g., it does not require complex methods, modeling or software); and
  • Evaluates the most pressing water quality problems.

Each year the grades are updated on a moving basis by dropping older data and adding newer data through the previous year. The grading systems are explained below.

Grading Coastal Waters: Buzzards Bay Eutrophic Index

APCC chose 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:

Embayments and estuaries often contain aquatic habitats that range from freshwater to brackish to salt marsh to open water bays bordering the ocean. For coastal embayments that contain salt marshes, the Buzzards Bay Coalition developed a variation of their scoring system. APCC’s scoring of salt marsh systems follows the approach used by the Buzzards Bay Coalition with additional input from salt marsh experts.

  • 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 CCMP; and
  • Evaluate the appropriateness of the Buzzards Bay Project’s recommended nitrogen limits.

In addition to the BBC, the Eutrophic Index has also been used by the Center for Coastal Studies, the Pleasant Bay Alliance, and the town of Chatham to evaluate nitrogen pollution in Buzzards Bay, Cape Cod Bay and coastal waters around the Cape, Pleasant Bay, and Chatham. The Eutrophic Index is considered by practitioners to be a well-tested method.

The Eutrophic Index scores parameters that measure the degree of eutrophication: dissolved oxygen saturation, water clarity (measured using either Secchi disk or a turbidity meter), chlorophyll, dissolved inorganic nitrogen (DIN), and total organic nitrogen (TON). Water quality data for these parameters is used to calculate a numerical score that indicates the degree of eutrophication. To translate scores into an assessment of water quality, the BBC uses three categories to “grade” scores: scores of 65 to 100 indicate Good water quality; scores between 35 and 65 indicated Fair water quality; and scores below 35 indicate Poor water quality.

Following the BBC’s method, APCC calculated numerical Eutrophic Index scores for water quality from stations in coastal embayments and coastal waters around Cape Cod. However, APCC “graded” the numerical scores for water quality from individual stations in a manner that differs from the BBC. APCC assigned scores to two grading categories based on whether they indicate acceptable water quality or unacceptable water quality. The two grading categories were chosen to indicate the type of action needed to protect or restore water quality.

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 took the additional step of identifying embayments where at least one monitoring station had Unacceptable water quality and graded these embayments as “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 summary of which embayments have portions with poor water quality that requires restoration vs. embayments with good water quality that require protection.

Grading Ponds and Lakes

Method 1: Carlson Trophic Index

To grade water quality in freshwater ponds and lakes, APCC uses two methods. The first method is the Carlson Trophic Index (CTI) which evaluates the trophic state of the water body in terms of three important water quality parameters: total phosphorus, chlorophyll, and water transparency. The Carlson Trophic Index was developed in 1996 to assess the trophic state of a freshwater pond or lake, where trophic state refers to the ecological response (algal biomass) to nutrients (Carlson, 1977). Since then, it has been widely used for evaluating freshwater ponds and lakes.

Using the Carlson Trophic Index, a pond with high nutrient concentrations (eutrophic to hypereutrophic) would be characterized by high concentrations of algae, algal scums, poor water clarity due to dense algae and low to no dissolved oxygen. A eutrophic to hypereutrophic pond would have scores between 50 and 100. At the opposite end of the spectrum, a pond with low nutrient concentrations (oligotrophic) would be characterized by clear well-oxygenated water, healthy aquatic plants and little to no algal growth. An oligotrophic pond would have scores between 0 and 40. A pond with intermediate nutrient concentrations (mesotrophic) would be characterized by moderately clear water, intermediate amounts of aquatic plants and algae, and low dissolved oxygen during the summer. A mesotrophic pond would have scores between 40 and 50. The Carlson Trophic Index is analogous to the Buzzards Bay Eutrophic Index in that it can be used to evaluate the degree of eutrophication in fresh water.

APCC adopted a grading system that assigns the following grades to Carlson Trophic Index (CTI) scores:

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

CTI 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 remain healthy and free of pollution.

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 for CTI scoring: Many datasets for pond water quality for Cape Cod ponds are older, i.e., at least five years old or more. Using older data to grade ponds would cause grades to reflect conditions that existed at the time when water samples were collected and analyzed. Conditions in ponds may have changed since such older data were collected. APCC screened out pond data older than 2016 and ponds where there was less than three years of data. In addition, since chlorophyll is a key component of the CTI grade, ponds where there was no chlorophyll data were not scored. As a result, this year there were 36 ponds with sufficient water quality data to grade. Application of these stringent data quality requirements for grading resulted in only 36 of 996 ponds having sufficient water quality data to enable grading using the Carlson Trophic Index. This points out the severe shortage of newer Cape-wide pond monitoring data to inform pond management and protection measures.

Method 2: Using Cyanobacteria Monitoring Data

Since 2018, APCC has been monitoring cyanobacteria and cyanobacteria blooms in dozens of freshwater ponds on Cape Cod. Cyanobacteria blooms occur when there are sufficient nutrients to stimulate growth of these photosynthetic bacteria. Warmth and sunlight are other factors that stimulate cyanobacteria growth, but in the absence of nutrients or when nutrient concentrations are very low, cyanobacteria growth is minimal. Cyanobacteria blooms therefore represent another way to describe nutrient enrichment in freshwater ponds.

APCC’s Cyanobacteria Monitoring Program uses 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). The EPA protocol utilizes a combination of field observations, microscopy and fluorometry to analyze samples from freshwater lakes and ponds for cyanobacteria. The data collected includes photographs and field observations, digital microscopy to identify composition (type of cyanobacteria present) and dominance, and concentrations of phycocyanin and chlorophyll pigments indicative of the amounts of cyanobacteria vs. general algae and phytoplankton, respectively. By monitoring biweekly from June to October, APCC tracks changes in cyanobacterial composition, dominance and abundance. At this sampling frequency, APCC is often able to forecast when cyanobacteria blooms may be forming or leading to toxin concentrations that may be approaching harmful levels. These signs instruct APCC to increase the frequency of testing and to inform town officials to be aware of potential threats and to plan for proactive management actions to protect public safety. To learn more, visit APCC’s Cyanobacteria Monitoring Program.

In contrast to traditional cyanobacteria testing involving cell counts, APCC’s method is less costly, offers a faster turn-around time for results and is often able to predict cyanobacteria bloom formation. Additionally, numerous other points of data collected support research efforts that will expand our understanding about the health of the ponds.

To address the shortage of recent pond water quality data, last year APCC adopted a second method of grading ponds using cyanobacteria monitoring data to provide an additional measure of pond health. The additional grading method helps to fill the gap in freshwater pond data by providing a different measure of trophic status. APCC’s cyanobacteria grading system utilizes our warning tier system for assigning monitored cyanobacteria concentrations into “Low,” “Moderate” and “High” tiers describing potential risks following ingestion of water by humans and pets. The previous year’s monitoring results are used. This year, APCC again utilized cyanobacteria data to grade ponds as described below.

Cyanobacteria grading system used in this 2021 State of the Waters report: In 2020 APCC revised our cyanobacteria warning tiers in order to better define risk in terms of exposure to children, pets, exposure during recreational activities, toxin concentrations, and presence of visible cyanobacteria blooms. The revision enabled a wider range of risks to be defined but still within a 3-tiered system:

  • “Low” (BLUE) indicates general safety for recreational activities according to our data.
  • “Moderate” (YELLOW) indicates the cyanobacteria concentrations in the pond are particularly dangerous to children or pets if ingested
  • “High” (RED) indicates APCC found either toxin levels approaching or exceeding state standards for recreation or found a visible cyanobacteria scum; each poses a considerable risk for human and pet interactions with the pond.

Using these tiers, APCC graded ponds in the “Moderate” or “High” tiers for cyanobacteria as Unacceptable, for the reasons given below:

  • APCC’s “Moderate” tier discourages children and pets from interacting with ponds due to cyanobacteria concerns.
  • The town of Barnstable posts “Pet Advisories” due to cyanobacteria concerns, cautioning parents and pet owners to keep children and pets away from the water, when a pond is in APCC’s “Moderate” tier.
  • In keeping with scientific consensus, APCC updated our warning tier criteria in 2020. The update resulted in 2020’s “Moderate” tier being similar to the “High” tier in 2019.

The resulting cyanobacteria grading system is as follows:

Cyanobacteria grades for 2020 ponds in the “Low” tier were graded as: “Acceptable: ongoing protection is needed”; and
Cyanobacteria grades for 2020 ponds in the “Moderate” and “High” tiers were graded as “Unacceptable: requires immediate restoration”.

Combined Pond Grading System

APCC’s combined pond grading system combinesdavailable Carlson Trophic Index grades and cyanobacteria grades, as described below and updated with more recent data and revised cyanobacteria grading system (see above):

  1. Carlson Trophic Index scores and grades for ponds were calculated only for ponds where more recent water quality data from 2016 on was available, and where at least three years of data were available.
  2. 2) Cyanobacteria monitoring data from 2020 were used to grade ponds using APCC’s revised tiered cyanobacteria system described above:
    1. Ponds in the “High” and “Moderate” cyanobacteria tiers were graded as “Unacceptable: requires immediate restoration”;
    2. Ponds in the “Low” cyanobacteria tier were graded as “Acceptable: requires ongoing protection.”
  3. If a pond had both Carlson Trophic Index grades and Cyanobacteria grades:
    1. The pond was graded as “Acceptable: requires ongoing protection” only if both grades were Acceptable;
    2. 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., Carlson Trophic 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 drinking water 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 chose to evaluate water quality and compliance of public water supplies after treatment and before distribution to consumers, the so-called “finished water.” This represents the underlying quality of the public water supply before it is distributed to customers, 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 chose to evaluate 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 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, APCC did a preliminary review of CCRs and decided to apply a revised grading system. The original and revised grading systems are described below.

Original grading system used in 2019 and 2020 State of the Waters: If a public water supply met all existing state and federal drinking water standards, it was graded as “Excellent” if not, it was graded as “Poor.” In the 2019 report on 2018 CCRs and the 2020 report on 2019 CCRs, all public water suppliers met all existing state and federal drinking water standards. Resulting grades were all “Excellent”.

Revised grading system used this year: Review of 2020 CCRs for Cape Cod public water suppliers showed that there were seven instances where public water suppliers reported that state and federal water quality standards were not met and/or required corrective actions. In particular there were varying degrees of potential risk posed by violations, e.g., ranging from one or two violations of the total coliform standard followed by compliance, to several violations of two standards occurring at different locations on different dates requiring issuance of a boil-water order representing a high potential risk level. APCC felt it was important to distinguish the different levels of potential risk. Accordingly, our public water supply grading system was revised to the following:

Excellent: Public water supply met all existing state and federal health and reporting standards (unchanged).
Good: Public water supply had one or more exceedance of total coliform MCL and/or no more than one violation of an existing state and/or federal standard that posed a risk to public health and that violation was neither chronic nor repeated.
Poor: Public water supply had two or more violations of an existing state and/or federal standard that posed a risk to public health or a violation that was repeated or persisted through more than one sampling round.


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. With the assistance of our Advisory Committee and partners, our sources of water quality data that met our criteria (see below) included the following organizations and agencies listed below. It is important to note that these organizations and agencies followed quality assurance protocols for sampling and analysis.

Regional data (i.e., data collected from multiple embayments or large regions of the Cape):

  • Association to Preserve Cape Cod: 2020 cyanobacteria monitoring data from ponds located in Barnstable, Brewster, Chatham, Dennis, Eastham, Falmouth, Harwich, Mashpee, Orleans, Sandwich, Wellfleet, and Yarmouth;
  • Barnstable Clean Water Coalition: coastal water quality data for the Three Bays watershed;
  • Buzzards Bay Coalition: Eutrophic Index scores for Buzzards Bay coastal stations;
  • Center for Coastal Studies: coastal water quality data for stations along coasts of 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);
  • Cape Cod Commission and University of Massachusetts at Dartmouth, School of Marine and Atmospheric Science and Technology (SMAST): Pond and Lake Stewards (PALS) data for pond water quality (note: most of the pond data provided by towns and organizations listed below was provided by PALS and SMAST for the towns and organizations);
  • Pleasant Bay Alliance: coastal Eutrophic Index scores for Pleasant Bay coastal stations;
  • Waquoit Bay National Estuarine Research Reserve (WBNERR): coastal water quality data for Waquoit Bay.

Municipal data:

  • Town of Barnstable: coastal water quality data, pond water quality data, and cyanobacteria data;
  • Town of Chatham: coastal Eutrophic Index scores for Chatham coastal stations;
  • Town of Dennis: pond water quality data;
  • Town of Eastham: coastal water quality data;
  • Town of Harwich: coastal and pond water quality data;
  • Town of Mashpee: coastal and pond water quality data;
  • Town of Orleans: coastal and pond water quality data;
  • Town of Sandwich: pond water quality data.

Types of water quality data are summarized below. The data can be found here: Resources.

Water quality data for coastal embayments: For this 2021 report, APCC collected the most recent and available coastal water quality data up to and through 2020 from the data sources listed above. Our criteria for grading coastal water quality data included at least 5 years of data from 2016 on (e.g., 2016, 2017, 2018, 2019, and 2020). There was one exception made: Harwich coastal water quality data where 2020 data were not collected due to suspension of their monitoring program due to the COVID-19 pandemic (data from 2015-2019 were used for grading).

Water quality data for ponds and lakes: Since 2000, the Cape Cod Ponds and Lakes Stewardship Program (PALS) has worked with volunteers and organizations who monitor many ponds across the Cape. The PALS program was developed by the Cape Cod Commission, APCC and SMAST, in coordination with organizations and towns that monitor water quality on an annual snapshot basis. Other pond associations and organizations have gathered a considerable amount of data with their member volunteers. For this 2021 report, APCC collected pond water quality data from the sources listed above. Our criteria for grading pond water quality data included at least three (3) years of data from 2016 on, and a requirement for chlorophyll data, as well as transparency and total phosphorus.

Cyanobacteria data for ponds and lakes: For this 2021 report, APCC utilized 2020 cyanobacteria monitoring data collected by APCC’s Cyanobacteria Monitoring Program and cyanobacteria data collected by the town of Barnstable for ponds in Barnstable.

Water quality data for public water supplies: For this 2021 report, APCC collected each town’s public-right-to-know reports for 2020 monitoring results, also known as the Consumer Confidence Reports (CCRs) for drinking water. CCRs are posted on each town’s website and links to the CCRs are provided in our Public Water Supplies grading. APCC used the CCRs for 2020 to grade water quality and compliance with existing drinking water regulations.


Our 2021 grades for coastal embayments and stations, freshwater ponds and lakes, and public water supplies are provided as maps and summarized in our table summarizing grades for 2019, 2020, and 2021. Detailed scores and grades for embayments, coastal stations, ponds, and public water supplies are provided in the spreadsheets under Resources. Our findings are described below.


Coastal embayments and coastal stations

Coastal embayments:

  • The 2021 embayment grades showed an increase in the number and percentage of Unacceptable embayments compared to previous years. There were 41 Unacceptable embayments, representing 87% of graded embayments. Last year in our 2020 report, 38 embayments or 79% were Unacceptable. In our 2019 report, 32 embayments or 68% were Unacceptable. (See summary of grades.)
  • The 2021 embayment grades showed a decrease in the number and percentage of Acceptable embayments compared to previous years. This year only six (6) of the 47 graded embayments were Acceptable, representing 13% of graded embayments. Last year in our 2020 report, 10 of 48 embayments or 21% were Acceptable. In our 2019 report, 15 of 47 embayments or 32% were Acceptable.
  • The three new Unacceptable embayments this year include two on Cape Cod Bay and one on Buzzards Bay.
  • There were 47 embayments graded this year, compared to 48 in 2020 and 47 in 2019.
  • There were no embayments that showed an improvement from Unacceptable to Acceptable.

Coastal stations:

  • The 2021 station grades showed an increase in the number of Unacceptable stations from previous years., with over two-thirds of stations graded as Unacceptable. There were 133 Unacceptable coastal stations, representing 68% of graded stations. In our 2020 report there were 106 Unacceptable stations or 70% of graded stations. In our 2019 report there were 98 Unacceptable stations or 64% of graded stations.
  • The 2021 station grades showed an increase in the number of Acceptable stations from previous years; however, the percentage of Acceptable stations was less than one-third of graded stations. There were 64 Acceptable coastal stations, representing 32% of graded stations. Last year there were 46 Acceptable stations or 30% of graded stations. In our 2019 report there were 54 Acceptable stations or 36% of graded stations.
  • There were 197 coastal stations graded this year, reflecting an increase from previous years. The increase in the number of coastal stations with sufficient data to grade was due to new data from several towns (e.g., Barnstable, Harwich, and others).


This year more ponds were graded (109) than last year (93). Only 36 ponds had sufficient water quality data to grade using the Carlson Trophic Index. To address the data gap, APCC used cyanobacteria monitoring data to grade 87 ponds. This resulted in 73 additional ponds being graded (there were only 14 ponds which both CTI and cyanobacteria grades). Results are summarized below, in the table summarizing results from 2019, 2020, and 2021, in the Ponds read-only spreadsheet, and in the static map of Pond grades.

  • The 2021 pond grades show that approximately one-third of all graded ponds were Unacceptable. There were 38 Unacceptable ponds, or 35% of all graded ponds. Last year there were 39 Unacceptable ponds or 42% of all graded ponds. In 2019 there were 58 Unacceptable ponds or 39% of all graded ponds.
  • The 2021 pond grades show that nearly two-thirds of all graded ponds were Acceptable. There were 71 Acceptable ponds, representing 65% of all graded ponds. Last year there were 54 Acceptable ponds representing 58% of graded ponds. In 2019 there were 91 Acceptable ponds or 61% of graded ponds.
  • A total of 109 ponds were graded this year using the Carlson Trophic Index and/or cyanobacteria tiers for cyanobacteria data collected in 2020. This represents only 11% of the Cape’s 996 ponds. Last year 93 ponds were graded using either the Carlson Trophic Index and/or cyanobacteria tiers. In 2019 a total of 149 ponds were scored; however, many of these had older water quality data (e.g., some dating back to 2003). For the 2020 and 2021 reports, APCC used stricter data quality standards, requiring at least 3 years of data from 2015 on and 2016 on, respectively.
  • This year only 36 ponds had sufficient water quality data to grade using the Carlston Trophic Index (i.e., at least three (3) years of data from 2016 on, including chlorophyll). Of these ponds, 24 or 67% were Acceptable and 12 or 33% were unacceptable.
  • This year a total of 87 ponds were graded using 2020 cyanobacteria monitoring data. Of these ponds, 52 ponds (60%) were Acceptable and 35 ponds (40%) were unacceptable.
  • Only 14 ponds had both Carlson Trophic Index and Cyanobacteria grades. Of these ponds with dual grades, six (6) ponds had Acceptable grades, and eight (8) had Unacceptable grades.
  • The percentages of Acceptable vs. Unacceptable grades for ponds graded using either the Carlson Trophic Index or cyanobacteria were as follows; 67% of ponds with CTI grades were Acceptable compared to 60% of ponds with cyanobacteria grades of Acceptable. Likewise, 33% of ponds with CTI grades were Unacceptable compared to 40% of ponds with cyanobacteria grades of Unacceptable. More data are needed to determine whether this similarity is incidental or reflects a more fundamental underlying commonality.
  • This year most of the ponds graded were located in the mid-Cape.

Public Water Supplies

This year APCC applied a revised grading system to grade public water supplies based on their 2020 Consumer Confidence Reports and state and federal drinking water regulations in effect in 2020 (see Grading Public Water Supplies). The results are described below, in the spreadsheet for public water supplies, and in the map of grades for public water supplies.

  • A total of 20 public water supplies were graded. (Note that the towns of Provincetown and Truro share a public water supply system which was graded as a single system).
  • Thirteen (13) public water supplies on the Cape continued to have Excellent water quality: Barnstable Fire District, Cotuit Water Department, Hyannis Water System, Otis Air National Guard Base, Brewster Water Department, Chatham Department of Public Works Water Division, Dennis Water District, Town of Eastham Water Department, Town of Falmouth Water Department, Town of Harwich Water Department, Mashpee Water District, Town of Orleans Water Department, and Provincetown Water Department.
  • Six suppliers were graded as having Good water quality: Barnstable Centerville-Osterville-Marstons Mills (COMM), Bourne Water District, Buzzards Bay Water District, North Sagamore Water District, Sandwich Water District, and Yarmouth Water Department.
  • One supplier (Wellfleet Municipal Water System) received a grade of “Poor” due to violations of two drinking water standards (E. coli and total coliform bacteria) and several violations at different locations which required the town to issue a “boil water order” to protect public health.

PFAS in public water supply wells was not graded because state and federal drinking water regulations requiring monitoring and limits on PFAS concentrations did not become effective until January of this year. APCC is monitoring the implementation of recently finalized regulations for PFAS and will apply these to public water supplies in the 2022 update of this report. It is known that increased testing in 2021 will reveal PFAS in public water supplies beyond what is currently know. The extent of the presence of PFAS in drinking water supplies will become an issue of greater public concern, discussion and expense in the year ahead. For more information on PFAS, see the PFAS Primer.


In 2019, APCC presented results of the first year of the State of the Waters: Cape Cod, an assessment of water quality in coastal embayments, ponds and public water supplies. The 2019 results were based on water quality data available through 2017. In 2020 APCC updated grades to incorporate data collected through 2019. This year, APCC updated water quality grades using water quality data available through 2020. Collectively these reports and this report show that the Cape’s coastal waters and ponds continue to suffer from eutrophication due to nutrient loading, primarily from septic systems. Public water supplies were generally excellent, but the exceptions indicate that public water supplies can still be vulnerable to bacterial contamination and, in one case (Yarmouth) to nitrite that was likely derived from septic systems and/or fertilizers.

Coastal embayments and stations

The increase in the number and percentage of Unacceptable embayments this year shows that coastal eutrophication continues and is expanding. For the first time, there were two new Unacceptable embayments (Barnstable Harbor, Quivett Creek) along the north coast of Cape Cod on Cape Cod Bay. The increase in the number of Unacceptable stations this year was likely related to an increase in the total number of stations graded combined with the percentage of Unacceptable stations (68%) remaining similar to last year (70%).

A number of towns have made significant steps toward managing nutrients by approving construction of modern wastewater treatment projects. While water quality has yet to improve as a result, as these projects are implemented over the next few years the region should begin to see lower nutrient loadings that should be reflected in improving water quality in selected embayments.


This year pond grades again indicated that approximately one-third of the 109 ponds monitored were Unacceptable.

As APCC’s monitoring has expanded much has been learned about the scope of the impairment of ponds. While lacking a sufficiently robust and lengthy data record upon which to base trend analyses, APCC is beginning to understand that while approximately one-third of ponds achieve Unacceptable status in any given year, that there is great variability year to year in which ponds trigger that designation. While the prerequisite conditions to impairment exist in many ponds, perhaps a majority of ponds Cape-wide, the actual confluence of events that drive poor water quality conditions in any given pond in a particular year remain hard to predict given the lack of detailed and multi-year data.

A comprehensive review and assessment of overall pond health is also hampered by data quality issues. To grade water quality, APCC uses the Carlson Trophic Index, an index of water quality that describes the trophic status of a water body based on total phosphorus, chlorophyll and transparency, (i.e., it is a measure of phytoplankton productivity due to nutrient loading where phytoplankton include algae and cyanobacteria). Many pond data are older, e.g., five years old or more. Using older data to grade ponds would cause grades to reflect conditions that existed at the time when water samples were collected and analyzed. Conditions in ponds may have changed since these older data were collected. This year APCC screened out pond data older than 2016 and ponds with less than three years of data collected. Using these more stringent requirements for grading resulted in only 36 ponds having sufficient water quality data to enable grading using the Carlson Trophic Index. This points out the severe shortage of more recent Cape-wide pond monitoring data to inform pond management and protection measures.

To help fill the gap in freshwater pond data, APCC utilized the results of our cyanobacteria monitoring program. Since 2018, APCC has been monitoring cyanobacteria and cyanobacteria blooms in dozens of freshwater ponds on Cape Cod. Cyanobacteria blooms occur when there are sufficient nutrients to stimulate growth of these photosynthetic bacteria. Warmth and sunlight are other factors that stimulate cyanobacteria growth, but in the absence of nutrients or when nutrient concentrations are very low, cyanobacteria growth is minimal. Cyanobacteria blooms represent another way to assess phytoplankton productivity due to nutrient enrichment in freshwater ponds and is complementary to the use of the Carlson Trophic Index. Of the 36 ponds with sufficient water quality data to be graded using the Carlson Trophic Index, 33% were Unacceptable. Of the 87 ponds graded using cyanobacteria tiers, 40% were Unacceptable. While 33% and 40% are not identical, the fact that the two grading methods yielded percentages of Unacceptable grades that were within 7 percentage points indicates that the cyanobacteria grades and the Carlson Trophic Index grades generally agree. This is consistent with the two grading systems measuring eutrophication, albeit in different ways: the Carlson Trophic Index measures phytoplankton while the cyanobacteria grade measures cyanobacteria (a component of phytoplankton).

Public Water Supplies

This was the first year since our State of the Waters program was initiated in which some public water supplies experienced contamination due to bacteria and in one case (Yarmouth) nitrite. In Wellfleet, repeated violations of E.coli and total coliform bacteria standards led to the town having to issue a “boil-water order” to residents in order to protect public health. These results show that ongoing vigilance is needed to protect our public water supplies from contamination by already-regulated contaminants such as bacteria and nutrients. In next year’s report, APCC will include PFAS as a regulated contaminant of concern.

Other water quality issues of concern

  • Consumer tap water quality was not evaluated and would require testing of the water coming out of consumers’ taps as well as monitoring data from water distribution systems. Water quality coming out of the tap will be affected by the age and type of pipes in the distribution system and in consumers’ homes and businesses.
  • Drinking water consumers and regulators alike need to consider that there may be other unregulated contaminants affecting drinking water quality. These include:
    • PFAS in drinking water and in aquatic ecosystems, from a wide variety of sources. APCC is monitoring the results of newly required PFAS sampling and will apply these to public water supplies when evaluating drinking water quality in 2021. Results will be reported in our 2022 State of the Waters: Cape Cod report. For more information on PFAS, see our PFAS Primer.
    • Emerging contaminants in surface water and/or groundwater:
      • Endocrine-disrupting compounds and pharmaceuticals from inadequately treated wastewater;
      • Microplastics from wastewater, stormwater runoff and atmospheric fallout;
      • Cyanobacteria (aka blue-green algae) in freshwater ponds produce toxins that are harmful to humans and animals if ingested. Public surface water supplies can become contaminated by cyanotoxins, and public water suppliers elsewhere are taking precautions to guard against cyanotoxins in drinking water. This issue is of limited scope on Cape Cod as only Falmouth utilizes a surface water source for a portion of its public drinking water. APCC has been monitoring cyanobacteria since 2018 and has incorporated cyanobacteria into our pond grading system since 2019.Harmful bacteria in coastal waters and freshwater ponds, lakes and streams include fecal coliform bacteria and enteric bacteria that are indicators of human and/or wildlife fecal matter. Bacteria can impact swimming beach water quality and water quality in shellfish beds. Beach water quality and shellfish bed water quality are monitored by Barnstable County and the state, respectively.
  • Mercury contamination of surface water continues to be of concern, based on the fact that this year 32 ponds and lakes on the Cape have fish consumption advisories due to high levels of mercury. Last year the number was 29, and the year before 24. Mercury originates from atmospheric fallout of mercury emissions from coal-burning power plants.
  • Climate change impacts for the Northeast are predicted to include warmer air and water temperatures year-round; more precipitation; more intense storms; longer and warmer growing seasons coupled with shorter and warmer winters; shifts in populations of fish, wildlife and invertebrates; rising sea level; changes in groundwater elevations; more flooding; and changes in dynamic landforms such as those found on the Cape (e.g., dunes, beaches, floodplains). Many of these climate change predictions will impact water quality and exacerbate the harmful effects of existing pollutants.

Filling the gaps: recommendations for monitoring

Monitoring is crucially important to understand current conditions and for tracking progress in improving and protecting water quality. Based on our findings, APCC provides the following recommendations for monitoring:

  • Coastal embayments need ongoing monitoring to collect up-to-date information on water quality in order to assess whether wastewater management measures and protection measures are working and to determine when success has been achieved.
  • Monitoring of at least four more coastal embayments is needed (Chase Garden Creek in Yarmouth, Red River in Harwich, Hatches Harbor in Provincetown, and Great Sippewissett Marsh in Falmouth). These embayments are listed in the 208 Water Quality Plan as coastal embayments receiving nutrients from their watersheds.
  • Pond monitoring should be expanded to many more ponds and lakes throughout the Cape, particularly those where there are swimming beaches, public access, and/or sensitive resources (e.g., diadromous fish, rare species, wildlife). The Cape Cod Commission has proposed a 208-scale study of ponds across the Cape. APCC strongly supports this initiative as responsive to the knowledge gaps around pond water quality and encourages the Barnstable County Commissioners and County Assembly of Delegates to approve this program early in 2022.
  • Cyanobacteria monitoring of ponds should be expanded as it provides a useful measure of eutrophication and a complement to water quality monitoring.
  • The PALS program is useful as a “screening tool” to identify ponds where more in-depth monitoring and assessment is needed to determine causes, extent and severity of problems. However, pond monitoring should be conducted more frequently than the once-a-year snapshot that is typically provided by the PALS program.
  • Newer, more recent pond data should be utilized to assess pond conditions and inform restoration and protection efforts.
  • Monitoring of pond water quality and cyanobacteria blooms should be conducted hand-in-hand so that water quality data can be used to help predict where serious cyanobacteria blooms may occur, and vice versa.
  • Public water suppliers should expand their monitoring of PFAS, emerging contaminants and cyanobacteria to help safeguard public health.


  • Despite the challenges and the need for much greater action in every town, there have been some successes in addressing nutrient pollution. These successes include the following:
  • Passage of state legislation in 2018 that established the Cape Cod and Islands Water Protection Fund to provide a non-property tax-based source of funds to help Cape Cod and the Islands pay for necessary wastewater infrastructure and water quality remediation efforts. In 2021 the first round of funding awards were awarded to a number of towns to assist them with wastewater management.
  • Barnstable County’s alternative septic system testing center has been testing efficacy of different alternative septic systems and has identified several as being potentially useful;
  • Sewer expansion projects in Chatham and in Falmouth;
  • Alternative wastewater treatment methods are being tested or utilized in towns, including permeable reactive barriers in Falmouth and Orleans and shellfish aquaculture projects in Falmouth, Barnstable, Mashpee, Yarmouth, Dennis, Orleans and Wellfleet;
  • Partnering agreements between towns to share public wastewater treatment facilities (e.g., Harwich and Chatham); including first-ever sewers installed in Harwich;
  • Groundbreaking in 2020 for the Orleans wastewater treatment facility and collection system;
  • The state’s first Watershed Permit for four towns in the Pleasant Bay watershed, designed to facilitate a coordinated effort by the towns of Brewster, Chatham, Harwich and Orleans and the Pleasant Bay Alliance to control nutrient pollution in Pleasant Bay (see Pleasant Bay Watershed Permit);
  • Intermunicipal agreement between Mashpee, Sandwich and Barnstable for nitrogen load sharing for the cleanup of Popponesset Bay;
  • Pond restoration success stories have been compiled by the Cape Cod Commission. Success stories for freshwater ponds are fewer because ponds have not received the attention that coastal embayments have received;
  • Additional water quality improvement success stories can be found on the Cape Cod Commission’s website.

Finally, ecological restoration projects provide benefits for water quality as well as ecological benefits for fish and wildlife habitat. Several restoration projects that are planned, underway or completed include: Parkers River tidal restoration, Herring River tidal restoration, Childs River freshwater wetland restoration, Coonamessett River restoration, Sesuit Creek salt marsh restoration, Three Bays stormwater remediation project, Stony Brook salt marsh and fish passage restoration, and others. APCC’s Restoration Coordination Center is assisting with many of these projects and provides Cape Cod communities with assistance in planning and implementing successful restoration projects. For more information on restoration projects on Cape Cod, visit APCC’s website.


Click on a map image below to open the corresponding PDF.

Embayment Status
Public Water Supply Status
Sewered Areas, Title 5 Septic System Areas, and Open Space Areas
Embayment Stations
Pond Status