Results

Coastal embayments

By using the Cape Cod Commission’s Water Quality Data Portal, we were able to include many more stations in the Eutrophic Index (EI) analysis—226 in 2023 to over 280 in 2025 (Fig. 2a, Fig. 3, Table 2). That broader coverage increased the number of embayments with grades from 48 to 51 (Fig. 2b). The three added embayments are Gunning Point Pond and Herring Brook in Falmouth and Paines Creek in Brewster.

While the overall number of stations has increased as a result of using the Commission’s database, the number of stations and parameters sampled still changes each year as a result of fluctuations in funding, access to watercraft or property, and volunteer or staff availability. Because the number or location of stations included in the sampling program is regularly in flux, understanding change over time in habitat quality is challenging. As seen in Figure 2a, the number of stations within a status category (acceptable, unacceptable, and insufficient data) shifts each year. It’s important to recognize that these shifts in station status are not likely an indication of improvement or degradation in the habitat condition, and that, more likely, the results are an indication that stations have been added or removed over time (see Table 2). In order to address this uncertainty, the number and location of stations must remain the same over the years. The importance of this point cannot be overstated; the value of monitoring water quality is greatest when methods are consistent year after year.

Table 2: List of the number of stations included in the State of the Waters analysis in 2021 through 2025 by embayment. Note: Even though the number of stations may remain the same, the location might have been modified over the years.

While the station results vary considerably in the annual comparison, the embayment status is largely unchanged over time (Figure 2b). In 2025, there were two acceptable and 48 unacceptable embayments, and one with insufficient data (51 monitored Cape Cod embayments total; Fig 5). This is only slightly changed from five years previous, in 2021, when there were two acceptable, 49 unacceptable, and one insufficient data (52 monitored embayments total). The additional Cape Cod embayment included in 2021 through 2023 was Gunning Point Pond in Falmouth. The only year that Gunning Point Pond had sufficient data to be included in the analysis was 2021.

The likely reason that station information can change but embayment status remains the same relates to the way embayment status is determined. The embayment status is based on the station with the lowest (worst) Eutrophic Index score; so as long as one station is unacceptable, the embayment status remains unchanged. In effect, station-level results are more sensitive to local conditions and monitoring changes, while embayment status is intentionally conservative: it does not improve until all reporting stations meet an acceptable threshold. This approach ensures that restoration or mitigation action is promoted as long as one station indicates an unacceptable habitat condition.

Figure 3 . Map of 2025 water quality grades for coastal stations. Water quality data for individual stations were scored using the Buzzards Bay Eutrophic Index and scores were grouped into acceptable and unacceptable categories (results represent data from 2010-2024).

The scale and impact of eutrophication on Cape Cod is not equally distributed among towns (Fig. 4). Falmouth, with the greatest number of embayments, faces a much larger task to mitigate impacts of wastewater pollution and restore water quality conditions to meet regulatory standards. While Brewster is relieved of the burden of poor water quality in coastal embayments, they do not escape the same underlying problem of leaching septic systems, but the detrimental effect is more directed towards freshwater ponds.

Figure 4 : The 2025 State of the Waters embayment status grouped by Cape Cod town. The embayment status is based on the lowest station Eutrophic Index score on a five-year running average. Water quality measurements influencing the scores provided were collected in 2020 through 2024. The three State of the Waters grading categories are as follows: unacceptable (Eutrophic Index Score <= 65), acceptable (Eutrophic Index Score > 65), and insufficient data (data do not meet qualification standards).

Individual embayment results are provided in Figures 5 and 6. The embayment status reflects the station with the lowest EI score within that embayment. Keeping in mind that stations fluctuate across years of sampling, Figure 6 clearly demonstrates the range of EI scores and how the embayments rank relative to one another. Where there are large differences between years within an embayment, this reflects a change in the available station data. Even with this caveat, there is no questioning the relative quality of these embayments. One pattern clearly emerges when looking at the data in this way. The largest embayments, such as Waquoit Bay and Pleasant Bay, rank among the worst, and smaller embayments, including Paines Creek and Quissett Harbor, maintain higher quality coastal systems. Tidal flushing and low residence time (high turnover) are likely factors in sustaining the healthier coastal embayments.

Figure 5 . Map of 2025 water quality grades for coastal embayments and the surrounding watershed. If there was at least one station in the embayment with Unacceptable water quality, the embayment received a grade of Unacceptable: requires immediate restoration. If all stations in an embayment had Acceptable water quality, the embayment received a grade of Acceptable: requires ongoing protection (results represent data from 2020-2024).

Figure 6 : Plot showing the annual minimum Eutrophic Index (EI) station scores (based on a five-year running average) within an individual coastal embayment on Cape Cod. The red dotted line indicates the threshold for State of the Waters grading; scores above 65 are considered acceptable, while scores below 65 are considered unacceptable. Note: The number and location of stations does not remain constant across years, so comparisons across years are meant to show range of variability but do not provide accurate trends of change over time.

Freshwater Ponds

Integrating the Cape Cod Commission’s Water Quality Data Portal to obtain freshwater pond data expanded the number of freshwater ponds with sufficient data needed to generate a Trophic State Index (TSI) score from 68 to 76. Starting next year, the number of eligible sites with sufficient data will increase to 116, augmenting the number of sites with TSI scores by close to half the current count. Figure 7 shows the additional sites which are currently shown as insufficient data but will become eligible next year. This massive jump in data is due to the development of the Cape Cod Regional Pond Monitoring Program, managed by the Cape Cod Commission and executed by APCC. The CCRPMP was initiated in 2023, but sites monitored under this program will not meet the three-year data requirement until the 2026 State of the Waters assessment.

While the number of ponds with unacceptable TSI scores has not changed significantly, the number of ponds with acceptable TSI scores has grown over the last five years (Figure 7). However, it’s important to note that the growing number of acceptable ponds may not be indicative of improved water quality and could, instead, reflect changes in the number of ponds assessed, sampling locations or monitored pond selection. Since monitoring programs are regularly undergoing modifications due to fluctuations in funding and adjustments related to access and staff or volunteer availability, comparing broad-scale habitat quality over time is challenging. Further analysis is required on a site-by-site basis to understand trends across years.

Figure 7 : The stacked bar plot above shows the total number of freshwater ponds that fall into three categories related to the Trophic Index Score (TSI) from 2021 through 2025: acceptable (TSI Score <= 50), unacceptable (TSI Score > 50), and insufficient data. Note these results do not reflect the FINAL pond status as cyanobacteria results are not accounted for here. In order to be included in the TSI analysis, data must be collected from June through September, include at least one measurement for each of the three required parameters, and have reoccurring sampling for at least three of the five previous years. Investigate the results more closely, by visiting the State of the Waters Data Viewer.

In addition to the TSI results, cyanobacteria monitoring data were combined with TSI scores to determine the final State of the Waters grading status (Fig. 8). The 2025 results from the combined datasets are available in Figures 8-10. The 2025 results only represent a small portion of the freshwater ponds within each of these towns. In total, there are 890 freshwater ponds on Cape Cod, and only a small subset of those ponds (158 or approximately 18%) were monitored and qualified for inclusion in the State of the Waters assessment.

Figure 8 . Map of 2025 water quality grades for freshwater ponds. Ponds were graded using the Carlson Trophic State Index and/or cyanobacteria data (results represent data collected in 2020-2024).

Figure 9 : Bar graph showing the number of ponds that received final gradings of unacceptable and acceptable in the 2025 State of the Waters (SOTW) assessment. Final grades are determined by a combination of five-year running Trophic State Index (TSI) score averages and cyanobacteria monitoring results from the previous year (i.e., 2024).

Figure 10 indicates how many of the ponds monitored received the final State of the Waters grade based on cyanobacteria only, TSI and cyanobacteria, or TSI only. By adding cyanobacteria monitoring data, the number of sites with final State of the Waters grades increases from 76 to 116. Barnstable has the highest number of monitored sites at 40 ponds, and Truro has the lowest number of sites at two ponds. For further information regarding which monitoring programs sample at each location, visit the Cape Cod Water Quality Data Portal. For individual pond information including which method determined the final grading and the underlying TSI parameter data, visit the State of the Waters Data Viewer and Appendix B.

Figure 10 : The horizontal bar graph demonstrates how the three differing methods were applied to generate the 2025 final State of the Waters grades for freshwater ponds in each Cape Cod town; TSI = Trophic State Index.

Public Water Supplies

Similar to previous years, the review of the 2024 Consumer Confidence Reports from public water suppliers (PWS) on Cape Cod shows that the majority of public suppliers continue to provide “Excellent” drinking water (Fig. 11 and 12). In 2024, 19 of the 21 facilities evaluated received an “Excellent” grade, meaning that all state and federal standards were met, and two received “Good” grades due to violations related to the total coliform standard. None of the PWS on Cape Cod received a “Poor” grade based on 2024 reports. However, PFAS6 was detected at 10 of the PWS on Cape Cod. New state regulations for PFAS6 concentrations became effective in 2021. None of the PFAS6 detections surpassed the state-regulated 20 parts per trillion maximum contaminant level (MCL), but the widespread detection of PFAS6 in public water supplies calls for ongoing monitoring as well as planning and implementation of effective treatment methods. Towns have either provided treatment to remove PFAS6 or are planning to provide treatment. For more information on PFAS, see APCC’s PFAS Primer.

Figure 11 : Results from the last five years of State of the Waters evaluations of Cape Cod public drinking water suppliers. State of the Waters grades reflect drinking water quality from the previous year. Note: The monitoring of PFAS began in 2022 when new state regulatory standards came into effect. Excellent grades indicate that all maximum contaminant levels (MCLs) were met throughout the year; Good grades indicate the finish water had one or more exceedances related to total coliform and/or there was no more than one violation of other MCL standards; Poor grades indicate that the finish water had two or more violations of MCLs that were repeated or persisted for more than one sampling.

Figure 12 . Map of 2025 grades for public water supplies of drinking water. Consumer Confidence Reports from 2024 were used to grade water quality in public water supplies prior to distribution to consumers. Asterisk indicates where PFAS were detected but were within state maximum contamination level.

The two PWS that received “Good” grades, Buzzards Bay Water District and the town of Wellfleet Municipal Water System, were in violation of the total coliform standard (Table 3 and Fig. 12). At the Buzzards Bay Water District, the 2024 report stated that there was a violation of the Total Coliform standard (the MCL is 0). A Level 2 assessment was required, and upon completion, no corrective actions were required. For the town of Wellfleet Municipal Water System, the 2024 report stated that there was a violation of the Total Coliform standard, where seven coliforms were detected in two rounds of sampling (MCL is 0). A Level 1 assessment was required. Upon completion of the assessment, four corrective actions were required; one was completed and three others were still in process. All other state and federal standards were met in 2024.

Table 3: The State of the Waters Public Drinking Water evaluation results. A single asterisk indicates PFAS detection, although it did not exceed the state maximum contaminant level (MCL). Conditional formatting is provided to highlight differences in grades across years and facilities. Excellent grades indicate that all MCLs were met throughout the year; Good grades indicate the finish water had one or more exceedances related to total coliform and/or there was no more than one violation of other MCL standards; Poor grades indicate that the finish water had two or more violations of MCLs that were repeated or persisted for more than one sampling. ** PFAS were not monitored in 2021.

Discussion

This is the seventh annual report on the State of the Waters: Cape Cod, which provides an assessment of water quality in coastal embayments, freshwater ponds, and public water supplies using the most recent available data. Collectively, these annual reports show that the Cape’s coastal waters and freshwater ponds continue to suffer from excess nutrients, primarily from septic systems located in the watersheds of the receiving waterbodies.

In contrast, public water supplies were largely “Excellent” with only two graded as “Good” and none graded as “Poor,” indicating that overall, the finish drinking water on Cape Cod is generally of high quality. Since new state regulations limiting PFAS6 concentrations in drinking water came into effect in 2021, the State of the Waters has monitored detections. While concentrations have not surpassed the 20 parts per trillion maximum contaminant level, the fact that nearly half of the public drinking water suppliers detect PFAS6 points to the need for ongoing monitoring, planning, financing, and implementation of effective treatment methods.

Coastal embayments and stations

Most of the Cape continues to be served by septic systems, with only small areas served by municipal sewers. Septic systems located in the watersheds of coastal embayments are the main source of excess nutrients in embayments. A number of towns have made significant steps toward managing nutrients by approving construction of modern wastewater treatment projects. While embayment 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.

Ponds

APCC’s understanding of pond water quality on Cape Cod has grown, but the geographic scope and environmental dynamics influencing the impairment are still largely unknown. Because long, consistent datasets are scarce, robust trend analyses are not yet possible. Recent data suggest that, in any given year, roughly one third of graded ponds receive an Unacceptable status, with considerable year-to-year variability in which ponds cross that threshold. Many ponds likely experience impairment conditions at times, but the specific combination of factors that produces poor water quality remains hard to predict without detailed, multi-year monitoring.

A comprehensive Cape-wide assessment of overall pond health is limited by both data quality and data availability. APCC grades ponds using two methods. The first is the Trophic State Index (TSI), which characterizes trophic status based on total phosphorus, chlorophyll-a, and water clarity (Secchi depth). Taken together, these parameters act as a proxy for phytoplankton productivity, including algae and cyanobacteria. Because many pond datasets are older (? 5 years), using them would reflect past conditions rather than current status. Thus, APCC applies data qualification standards (all parameters must be collected within at least three of the past five years) to capture reliable and recent conditions for the annual report. For 2025, the screening process yielded 76 ponds (out of approximately 890 on Cape Cod) with sufficient data to compute a 2025 TSI score. This underscores the significant shortfall in Cape-wide monitoring needed to inform pond management and protection.

To partially fill the gap in freshwater pond data, APCC applies a second method incorporating cyanobacteria (harmful algal bloom) risk. When data are available, the cyanobacteria risk indicator, which is based on toxin/advisory records or chlorophyll-a thresholds, can provide a supplemental means of evaluating impairment in freshwater ponds. By adding cyanobacteria monitoring data, the number of sites with final 2025 State of the Waters grades increased from 76 to 116.

There are three critical differences between the methods. TSI accounts for all phytoplankton productivity (provided by chlorophyll-a measurements) while the cyanobacteria grade measures cyanobacteria productivity only (provided by measurements of phycocyanin). TSI incorporates data from the past three to five years, while the cyanobacteria grade represents monitoring data from the previous year only. TSI aggregates measures of water quality, whereas cyanobacteria blooms represent the biological response to water quality and, importantly, weather.

Other water quality issues of concern related to coastal and freshwater ecosystems

• 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. Bacteria in beach water quality and shellfish area water quality are monitored by Barnstable County and the state Division of Marine Fisheries.
• Mercury contamination of surface water continues to be of concern. Eleven of the fifteen towns on Cape Cod had fish consumption advisories related to mercury as of January 2025: Barnstable, Bourne, Brewster, Dennis, Falmouth, Harwich, Mashpee, Orleans, Sandwich, Truro, and Wellfleet (MA Fish Consumption Advisories). Mercury originates from atmospheric fallout of mercury emissions from coal-burning power plants.
• PFAS contamination of surface water is also a concern. As of January 2025, five of the fifteen towns on Cape Cod had fish consumption advisories related to PFAS including Bourne, Falmouth, Mashpee, Sandwich, and Yarmouth (MA Fish Consumption Advisories).
• Predicted climate change impacts for the Northeast 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 changes will impact water quality and exacerbate the harmful effects of existing pollutants.
• Degrading polystyrene foam, traditionally used as flotation for docks and swim floats, has been observed washing up on the shorelines of freshwater ponds and coastal waterways, contributing to microplastics in these ecosystems. Several local pond groups and other local organizations are raising awareness of this problem, and some towns have enacted regulations banning exposed polystyrene foam and requiring encapsulated floats.

Public Water Supplies

The majority of public water supplies (19 of 21) met all existing state and federal drinking water quality standards and were graded as “Excellent.” The two exceptions graded as “Good” due to total coliform indicate that the potential for bacterial contamination always exists and monitoring is always needed. There were no “Poor” grades for 2024 drinking water reports. While PFAS6 was detected in 10 of the 21 public water supply systems, all 11 of these systems met the state’s PFAS6 standard. The widespread detection of PFAS6 in public water supplies calls for ongoing monitoring as well as planning and implementation of effective treatment methods. Towns either have provided treatment to remove PFAS6 or are planning to provide treatment.

Other water quality issues of concern related to drinking water

• Private wells were not addressed in this project. APCC strongly recommends that private well owners have their water tested and, if needed, treated.
• 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:
  • 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; and
  • A number of freshwater cyanobacteria species produce toxins that are harmful to humans and animals if ingested. Public surface water supplies can become contaminated by cyanobacteria and cyanotoxins, and public water suppliers who utilize surface water are required by state and federal laws 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.
• Climate change may also impact public water supplies through protracted drought.
• Continued development of land in drinking water protection areas is a threat to water quality. With only 14% of Cape Cod land left undeveloped and unprotected, and with most of that remaining unprotected land located within critical natural resource areas, it is vital that towns prioritize efforts to acquire and protect land within these sensitive resource areas. See APCC’s “Hanging in the Balance” report for more information.

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 four more coastal embayments is needed: Red River in Chatham and Harwich, Hatches Harbor in Provincetown, Great Sippewissett Marsh in Falmouth, and Salt Pond in Falmouth. These embayments are listed in the 208 Water Quality Plan as nutrient-impacted coastal embayments.
• In late 2022, APCC was contracted by the Cape Cod Commission to conduct the Cape Cod Pond Monitoring Program to monitor 50 ponds seven times per year for three years to collect water quality data. Monitoring got underway in early 2023, however, 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).
• Cyanobacteria monitoring of ponds should be expanded to more ponds, as it provides a useful measure of eutrophication based on cyanobacteria and complements conventional water quality monitoring. Monitoring of pond water quality and cyanobacteria blooms should be conducted in tandem so water quality data can be used to help predict where serious cyanobacteria blooms may occur.
• 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. The Cape Cod Pond Monitoring Program is an example of a more comprehensive pond monitoring program, and more towns and organizations should support and participate in this program.
• Public water suppliers should expand their monitoring of PFAS, emerging contaminants and cyanobacteria to help safeguard public health.