Monitoring Projects

The Waquoit Bay Reserve studies how what we do on land can affect the quality of our water in our bays and ocean. A major advantage of the Reserves over many research institutions is that we are place-based – that is, we own and manage land. This enables us to carry out long-term monitoring of the different ecosystems to observe change over time, and compare results across geographic regions. Waquoit Bay Reserve manages almost 3000 acres of land and water in Falmouth and Mashpee, including protected bays, barrier beaches, fresh- and saltwater marshes, streams, forest, and fields. By monitoring both abiotic (non-living – like weather, water quality, coastal erosion, and land use) and biotic (plants and animals) factors, researchers can examine relationships between the two, helping answer questions like:

  • What is the effect of suburbanization on water quality?
  • How does poor water quality affect how many winter flounder are hatched?
  • How quickly are invasive species spreading?
  • Has trout restoration been successful? How does that relate to water quality and stream flow?
  • What are the effects of sea level rise on salt marsh vegetation?
  • How are the rare plants and animals on the Reserve doing? Is climate change affecting that?

SYSTEM-WIDE MONITORING PROGRAM (SWMP – pronounced “swamp”): All 28 Reserves carry out SWMP, using the same protocols. Programs include weather, water quality, habitat mapping, salt marsh vegetation, and submerged aquatic vegetation. (See Research Sites for locations of permanent stations). These data are available from the Centralized Data Management Office:


  • Weather: The Reserve weather station measures temperature, wind speed and direction, barometric pressure, precipitation, sunlight and atmospheric conditions.
  • Water quality: The Reserve uses four automated dataloggers to monitor physical and chemical variables at 15-minute intervals. Measures of water quality include temperature, water depth, salinity, pH, dissolved oxygen, and turbidity. The Reserve periodically takes samples at one automated datalogger to measure nutrients (ammonium, nitrate, nitrite, ortho-phosphate, and chlorophyll a).

Click here for an analysis of 16 years of trends derived from the system wide monitoring program, by Research Coordinator, Megan Tyrrell in 2017.  She examined the water quality data to determine if, for example, critical temperature thresholds  affecting organism growth or survival have been crossed during crucial times of the year. Additionally, she presented some meteorological data analyses that examined whether the increase in extreme precipitation events have led to salinity drops or turbidity spikes near the salt marsh water quality monitoring station.

Habitat mapping:  Aerial surveys were flown in 2004 and 2012. Subsequent, dedicated habitat mapping aerial surveys will take place as funding allows. Vegetation types are mapped from the images. Results are field-checked, and maps are compared with previous surveys to see what changes have occurred. Click below for Maps of 2004 survey.

Tim’s Pond      Jehu Hamblin marsh     Waquoit Bay     The Dog (South Cape Beach)     Sage Lot Pond (South Cape Beach)     Abigail marsh

Salt marsh biomonitoring: Surface elevation tables have been installed and monitored annually at Sage Lot Pond in the South Cape Beach salt marsh, plant species are recorded by percent cover and density. In addition, certain physical variables are also recorded, OLYMPUS DIGITAL CAMERAincluding relative marsh surface elevation and groundwater depth, temperature, and salinity. Human impacts (e.g., nutrient enrichment or tidal restrictions) and environmental stressors (e.g., climate change effects such as precipitation rates and sea level rise) can drastically alter the spatial distribution and species composition of salt marsh plant communities. Changes in the biological structure of the marsh can result in reduced habitat and function. By closely monitoring the biological and physical variables of salt marshes over time, coastal researchers and resource managers will have a better understanding of how these estuarine systems respond to particular disturbances, and consequently, will be better equipped to protect the future health and integrity of coastal marshes.

What’s Up with the Water in Waquoit Bay (presentation)
One of Dr. Tyrrell’s first orders of business when she joined the Reserve 2016 was to analyze the wealth of over 20 years of water quality monitoring data the Reserve has collected. She has discovered  trends in temperature, salinity, and dissolved oxygen that could have implications for seagrass and harmful algal blooms as well as fish and crabs in the bay.
Communicating Results from the Tidal Marsh Resilience Synthesis to the Research Reserves, National Partners, and Coastal Managers (fact sheet)

Assessing tidal marsh resilience to sea-level rise at broad geographic scales with multi-metric indices (fact sheet)

wb_beachSubmerged aquatic vegetation (SAV – macro-algae and eelgrass): One of the biggest contributors to poor water quality on Cape Cod is the addition of too much nitrogen to the bays. Septic systems are the primary source (only about 15% of the Cape is sewered, and septic systems do almost nothing to remove nitrogen), though fertilizer and air pollution also play a role. Delivered to the bay by groundwater or surface run-off, the nitrogen acts as a fertilizer leading to large algae blooms, which shade and kill eelgrass and deplete oxygen from the water. Surveying the distribution and species composition of SAV over time helps illuminate how this process may be changing in Waquoit Bay, revealing, for example, if new species of algae are becoming dominant, whether the little remaining eelgrass is disappearing, or whether climate change is affecting SAV distribution. Thus, the survey helps determine how natural and/or human-caused factors may influence the overall health and sustainability of the estuarine system. The third SAV survey was completed in 2011.


Bay Watchers: Initiated in 1993, the WBNERR Bay Watcher program is comprised of volunteer, citizen-based 2012-06-26_08.31.02monitors who conduct field sampling and water quality measurements throughout the year. These monitors measure several key environmental parameters (such as temperature, salinity, dissolved oxygen, nutrients, and chlorophyll) in Waquoit Bay and its associated water bodies. WBNERR Bay Watchers form a key data collection component of the WBNERR Water Quality Database. Bay Watcher data expands geographic coverage of water quality sampling throughout the entire watershed, and provides comparative data at our 3 SWMP stations.

Click here for a 2016 analysis of 20 years of trends derived from the Bay watchers volunteer water quality monitoring data, by Research Associate, Jordan Mora.  Her trends analyses indicated increased temperatures and declining dissolved oxygen from this volunteer based program. The implications for these climate change related trends in combination with on-going, well documented nutrient pollution in Waquoit Bay, were discussed.

Pond Watchers: Volunteers from the organization Falmouth Associations Concerned with Estuaries and Saltponds (FACES) collect water samples from the south- and west-facing facing saltponds in Falmouth on a weekly basis. They measure temperature, salinity, dissolved oxygen and turbidity. Results are analyzed with Reserve staff help and reported weekly in the Falmouth Enterprise. This program broadens the geographic reach of the Reserve’s water quality collection, and keeps awareness of the weekly changes in water quality front and center through local media.

USGS Stream Gauge program – Quashnet River: USGS and other federal and state agencies monitor stream/river flow throughout the US using stream gauges. The data has a high importance for all water resource managers as well as emergency managers in case of flood conditions. Data on QuashnetRiver flow – the largest freshwater input into WaquoitBay – is highly valuable environmental information for WBNERR researchers. The Quashnet River gauge is currently the only one on Cape Cod. While this program is not operated by WBNERR, it is located within the Reserve and on Reserve land, and monitors the Reserve’s most important fresh water stream. Due to budget cutbacks, there have attempts, in the past, to eliminate this important station from the program. This and the SWMP programs are both part of the National Hydrometeorological Data System. WBNERR has high interest in seeing this important monitoring program maintained.

River Instream Flow Stewards (RIFLS): Managed by the MA Division of Ecological Restoration (DER) (formerly Riverways). RIFLS is a program that enables local groups to learn about the importance of healthy streamflow, document streamflow on otherwise un-gauged rivers and restore more natural flow regimes in rivers suffering from abnormal flow alterations. Streamflow data are essential in determining suitability of rivers for fish restoration, specifically sea-run brook trout and river herring. WBNERR cooperates with DER, Falmouth Rod and Gun Club, and Department of Fish and Wildlife. To monitor a gauge they installed on the Childs River: (http://www.rifls.org/detail.asp?siteId=64)


JimNDchicksEndangered Shorebirds: Protecting rare shorebirds is a collaborative effort from various biologists, private organizations, state agencies, beach managers, and volunteers. The Waquoit Bay Reserve has participated in rare shorebird monitoring and conservation efforts since 1990. WBNERR monitors South Cape Beach and Washburn Island, which are part of the Reserve, and also private nesting areas at New Seabury Beach and the Menauhant Yacht Club Beach.  Population monitoring serves as an integral aspect of recovery efforts for an array of shorebirds. It allows wildlife managers to identify limiting factors, assess effects of management actions and regulatory protection, and track progress toward recovery. Actively protecting piping plovers (Threatened) and least terns (special concern) at WBNERR also protects the beach, dune and marsh habitats for many species of wildlife including a wide variety of shorebirds and rare tern species that use the barrier beach and coastal salt marsh system to feed, nest or stopover during spring/fall migrations. Arctic, Common, Roseate and Least Terns rest on our beaches and forage in the waters off South Cape and Washburn Island. Nearby Buzzards Bay, hosts the largest Federally Endangered roseate tern colony in North America.

Horseshoe Crab spawning survey: Horseshoe crabs are counted in a known spawning area during the full and new-moon high tides in May and June as part of a regional effort to characterize the spawning population and to summarize a relative spawning index over time for the species. The survey was started in response to concerns that HSC populations may be declining due to habitat loss and harvest pressure. Our survey is one of many state and New England-wide. The MA Division of Marine Fisheries compiles data from Massachusetts to assess trends in the spawning population and inform management decisions See: http://www.mass.gov/dfwele/dmf/programsandprojects/horseshoe_crab.htm#hcrab

Breeding birds: Birds are commonly used as sensitive environmental indicators. While, birds are only one of several types of organisms that inhabit salt marshes, they can yield insight that may be overlooked by studying only plants, invertebrates or fish. In 2000, the Reserve launched a volunteer-based effort to monitor the populations of breeding birds in three areas of the Reserve; the Quashnet River, Abigail’s Brook and Sage Lot Pond. Monitoring the population of breeding birds over time can give managers information on changes in vegetation, prey abundance, predation pressure, and changing climate.John Harrison osprey With fish

Osprey: Like many raptors, this once-endangered bird has made a spectacular comeback since banning the pesticide, DDT. A total of 37 osprey nest sites have been located in the areas around Waquoit Bay and mapped using GPS coordinates. The occupied sites are visited once monthly from April through Aug/ September by staff and volunteers to record activity and document the number of chicks fledged from each nest. In 2011, the project also included the repair of several nesting platforms. WBNERR’s data is incorporated into regional nesting data compiled by Mass Audubon Society. (Osprey Photo by J. Harrison)

New England Cottontail rabbit: This native species is separate from the introduced Eastern Cottontail rabbits typically seen in open areas. New England Cottontails need dense underbrush to survive. As forests mature and shade out brush, or land is cleared for housing, this habitat has become increasingly rare, resulting in a disappearance of these rabbits from 86% of their former range. In an effort to keep it off the endangered species list,  US Fish and Wildlife Service is documenting species occurrence, population estimates, and recovery efforts.  Cape Cod and especially Mashpee (including Reserve land at South Cape Beach) contain some of the largest populations of the species in New England. Monitoring consists of trapping, tagging, collaring, and tracking individual rabbits.  It also includes pellet collection and DNA analysis for species identification.  Field work is done primarily in the winter.  (http://www.fws.gov/northeast/indepth/rabbit/index.html).

A New England Cottontail success story highlighting three Mashpee NEC projects  can be found on the Massachusetts Natural Resource Conservation Service website. Mashpee River Reservation (TTOR), Carl Monge Sanctuary (Orenda Wildlife Land Trust) and the Mashpee Wampanoag Tribe:  http://www.nrcs.usda.gov/wps/portal/nrcs/detail/ma/newsroom/stories/?cid=stelprdb1259979.

Trout: Brook trout are the only trout native to eastern North America and are considered an indicator species because they are sensitive to change in the environment.  Historically very common in this region, the brook trout is now classified as “reduced”, “greatly reduced” or “extirpated” from its original home waters in eastern Massachusetts, which is indicative of the degree of modification to their original habitats.  Together with MA Fish and Game and Trout Unlimited, we track movement of tagged fish throughout the watershed. Animal tagging studies help us understand individual movement behaviors, the size of home ranges, migration patterns, habitat usage, and population characteristics.  Understanding these factors can inform conservation decisions pertaining to many species, but is particularly important when dealing with anadromous fish, such as sea-run brook trout, because of their complex life histories. (http://www.capecodtu.org/QUASHNET_RESTORATION.html)

Fish survey: The Massachusetts Division of Marine Fisheries (MDMF) has carried out an annual seine (net) survey in six Cape Cod estuaries (including Waquoit Bay) since the mid-1970s with the primary mission of assessing the new young-of-the-year winter flounder population. The results are used to assess how this valuable commercial and recreational species is doing. While carrying out this regular survey, MDMF has also recorded detailed data on a number of other species as well including Blue Crab and Green Crab. Interestingly this database spans a period of notable habitat decline, particularly a major reduction in eelgrass, within most of these Cape Cod estuaries. The dataset represents the longest, most detailed, and most rigorously maintained biological record of estuarine species for Cape Cod.  http://www.mass.gov/dfwele/dmf/programsandprojects/resource.htm#resource


In addition to the SWMP SAV survey, the Reserve monitors two rare plant species.  Agalinis acuta (sandplain gerardia) and Liatris borealis (New England blazing star) are monitored annually with help from the Massachusetts Natural Heritage/ Endangered Species Program. Agalinis, with fewer than 15 known sites, is on the Federal endangered species list and Liatris is a state-listed plant of special concern. http://www.centerforplantconservation.org/collection/cpc_viewprofile.asp?CPCNum=36