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Shellfish Beds

Extent Condition Protection/Restoration


Bivalve mollusks such as oysters, sea scallops, razor clams, and soft-shell clams, often aggregate in dense groupings, forming a habitat type known as shellfish beds. Some shellfish, such as the blue mussel, secrete strong, flexible strings ("byssal threads"), enabling them to anchor to hard surfaces, including other shells. Other species, such as scallops, soft-shell clams, and razor clams, do not physically attach to each other, yet these aggregations are also referred to as shellfish beds. The variety of bivalves found in shellfish beds indicates these habitats are found at varying depths, salinities, and/or substrates.

Shellfish beds provide many habitat services including refuge for smaller organisms such as polychaete worms, juvenile crabs, snails, and sea stars. Additionally, organisms such as slipper shells, sponges, and algae can attach to shells' hard surfaces in areas otherwise dominated by soft sediments.

Figure 1: Blue mussels (A. Trepte)
    "Humans, crabs, lobsters, fish, and diving seabirds all consume large quantities of shellfish. For coastal residents and tourists, clamming is an important pastime, while for commercial fishermen in Massachusetts, shellfish beds support a significant fishery. Through filter-feeding, shellfish improve water quality by removing suspended material and particulate pollutants from the water column. Shellfish beds also provide an important link between benthic (bottom) and pelagic (open water) habitats by capturing small food particles from the water column and transferring them to the benthos (Donovan, et al., 2005)."

Shellfish beds in Boston Harbor were historically significant both in terms of their extent and their contribution to people's diets and incomes. With deterioration of water quality, continued harvesting pressure, and changes resulting from damming rivers, the health and number of shellfish beds began to decline. Today, efforts are underway to bring back some of the populations – for food and for shellfish's ability to filter water. Nevertheless, only a handful of people now make their living harvesting shellfish from Boston Harbor.

Shellfish beds provide many important ecosystem services including:

  • Sediment stabilization: Beds of shellfish (especially those of oysters and mussels) act to buffer the impacts of erosion related to waves, boat wakes, and currents.
  • Habitat: The structure of shellfish beds provides refuge, settlement substrate, and foraging grounds for many other types of marine life.
  • Food provisioning: shellfish serve as a source of food for birds, marine organisms, and humans. Soft-shell clams from Boston Harbor must go through depuration before being consumed by humans. Soft-shell clams are the only shellfish which are harvested from Boston Harbor for human consumption.
  • Carbon sequestration: The shells of shellfish naturally absorb carbon as they grow, thus helping to sequester carbon.
  • Water quality and nutrient cycling: Shellfish are important to water quality for two main reasons. First, mussels serve as indicators of water quality and are monitored by the Gulfwatch Program as well as the Massachusetts Water Resource Authority. Second, the process of filter feeding removes microscopic particles (phytoplankton, contaminants, etc.) from the water, improving turbidity, light penetration, and overall water quality as well as serving as a source of nutrients. These water quality improvements, in turn, contribute to improved habitat conditions for other organisms.
  • Employment: In addition to directly employing those who harvest shellfish, those involved in the processes of shucking, depurating, and selling shellfish also receive financial benefits from Boston Harbor's shellfish resources.


Shellfish beds are found throughout Boston Harbor although the diversity and make-up has changed with the uses and habitat quality of Boston Harbor.

MORIS DEP Shellfish
The Massachusetts Division of Marine Fisheries (DMF) identifies suitable habitats in Boston Harbor for the following native species: blue mussel, soft-shell clams, razor clam, and quahogs.

Suitable habitat has also been identified for European oysters. American oysters, which used to be present in great quantities, are virtually non-existent in Boston Harbor today. To understand the extent of shellfish bed habitat, it is first important to understand the different habitat needs of the different species of shellfish in the Harbor.

Shellfish suitability
Figure 2: Shellfish suitability in Boston Harbor region (MassGIS)

Blue mussels attach to hard surfaces, including other mussel shells. The blue mussel's habitat ranges from flat intertidal and subtidal areas to vertical surfaces.

Rather than attach to a hard surface, soft-shell clams burrow into soft mud and sand, coarse gravel, and compact clay substrates. Soft-shell clams survive in intertidal and subtidal areas (up to 199 meters in depth) and where salinity is between 10-33 ppt (Newell, 1986).

Razor clams also live in intertidal and subtidal areas and burrow into fine- to medium-grain sand and muddy sand (without silt). They can live in dynamic areas with unstable substrates.

(Leavitt, et al.)

Northern quahogs, which once served as a form of Native American currency, are believed to exist in Boston Harbor, as are ocean quahogs; but little information is available about either species' current population and reproductive successes. Quahogs burrow into muddy and sandy sediment, with the northern quahog occupying shallower waters than the ocean quahog. Both require areas with moderate tidal movement, adequate dissolved oxygen levels and dense concentrations of plankton.

American oysters used to be prolific in the Boston Harbor area, serving as an important food source and supporting a significant fishery. Their shells appear in great numbers in the oldest middens of the Harbor Islands and in the middens of the Back River. Although no longer common in Boston Harbor, records show that oysters were most abundant at the mouth of rivers such as the Charles and Neponset. Filling in tidal flats to create upland areas and damming the mouth of the Charles River (which, among other things, impacted salinity and sedimentation) led to the depletion of American oysters in the vicinity of downtown Boston. Archaeological studies have shown that oysters may have been present in the Dorchester Bay area into the 20th century, but research is inconclusive as to exactly why those beds disappeared. Anecdotal reports, however, indicate that natural American oyster reefs may be present in the Back River, along the Squantum Penninsula, and in Savin Hill Cove.


Most shellfish beds in Boston Harbor are exposed to one of many threats associated with their close proximity to an urban area, helping to explain why virtually all species of shellfish in Boston Harbor have declined since the 1600s and 1700s.

    "Reduced water quality is the biggest threat to nearshore shellfish beds, with high levels of nutrients, excessive sedimentation, toxics [sic], and increased water temperatures [are] all factors that contribute to diminished water quality. Outbreaks of disease and parasites have been implicated in the severe declines of coastal oyster populations, and reduced water quality and increased salinity are thought to contribute to the success of these pathogens. Overfishing of shellfish can also diminish their filtering function, potentially leading to increased turbidity (cloudiness due to sediments or other substances in the water) and diminished light penetration to the seafloor. Shellfish beds can be destroyed if they are dredged or if dredged material is deposited nearby or in upstream locations. Bottom-tending fishing gear, such as trawls, also harms shellfish beds through direct physical damage and re-suspension of sediments, which can slow growth rates or even smother filter-feeding shellfish" (Donovan, et al., 2005).

One measure of shellfish condition is whether the animals are suitable for human consumption. The DMF classifies shellfish growing areas as follows:

APPROVED Open for harvest of shellfish for direct human consumption subject to local rules and state regulations.
CONDITIONALLY APPROVED During the time that the area is approved, it is open for harvest of shellfish for direct human consumption subject to local rules and state regulations.
CONDITIONALLY RESTRICTED During the time that the area is restricted, it is only open for the harvest of shellfish with depuration subject to local rules and state regulations.
RESTRICTED Open for harvest of shellfish with depuration subject to local rules and state regulations or for the "relay" (the transport of animals to other locations) of shellfish.
PROHIBITED Closed for harvest of shellfish. This includes areas identified as being under the former "management closure" classification

In Boston Harbor, shellfish growing areas are predominantly classified as prohibited with some small areas only conditionally restricted.

  • 27,488 acres of Boston Harbor's shellfish beds are classified as PROHIBITED (approximately 89% of the project area
  • 3,350 acres of Boston Harbor's shellfish beds area classified as CONDITIONALLY RESTRICTED (approximately 11% of the project area)
Figure 3: Designated shellfish growing areas. Red indicates the shellfish beds are 'prohibited', orange indicates 'management closure' and yellow indicates 'conditionally restricted' (MassGIS)

Soft-shell clams harvested for human consumption from Boston Harbor must go through depuration prior to being sold. Depuration is the purification of shellfish at an off-site facility where the harvested shellfish filter clean seawater for at least three days before undergoing a series of tests to ensure that all contaminants have left their bodies. Soft-shell clams from Boston Harbor are sent to a special facility in Newburyport, MA to undergo depuration. The depuration facility in Newburyport has been in operation since 1928, and it processes approximately 560 bushels of soft-shell clams per week.

Data Gaps

While much is known about the habitat conditions that shellfish need for survival, a considerable data gap exists in the lack of knowledge about the locations of existing and historic beds. While some beds have been identified, several known beds have not been mapped, and many more are believed to exist but have not been verified. The Office of Coastal Zone Management (CZM), however, is currently reviewing images taken during the US Geological Survey's (USGS) survey of "Boston Harbor and Approaches." CZM has identified mussels in several images from the survey, which was conducted in order to ground truth information used to develop a physiographic map for the region at depths between 2.5 and 29.8 meters (Ackerman, et al., 2006). The spatial data will be made available in early 2012.

In terms of identifying a comprehensive list of shellfish beds, it has been suggested that using the presence of predatory bird species as indicators of shellfish beds would be appropriate. Since shellfish beds are growing and shrinking on an ongoing basis, this data layer would need to be maintained frequently maintain accuracy.

Additionally, as mentioned below, one way to protect and/or restore shellfish beds is to remove nearby stressors that may affect the habitats. While information is known about some of the stressors in Boston Harbor (e.g. tidal restrictions, nutrient loading, etc.), there is little information available directly tying those stressors to current and/or historic shellfish beds. This knowledge would be very useful in targeting future protection and enhancement efforts.

Protection and Restoration Potential

Shellfish bed enhancement projects are conducted in Boston Harbor to address water quality issues and to improve commercial shellfishing opportunities. In 2006, the MA Division of Marine Fisheries initiated a soft-shell clam enhancement project with the communities of Winthrop, Quincy, Weymouth, Hingham and Hull. This project was intended to increase the number of soft-shell clam beds available to licensed fishermen within three years of each bed's planting. The first year provided several important insights about site selection and seed size, and in 2007, DMF planted 870,000 additional juvenile clams. The program continued in 2008; and by 2011 they had planted more than six million clams at twenty-eight sites throughout five communities (Bettencourt, 2011). In October 2010, restored beds at Casey's Beach in Hull were re-opened to licensed master and subordinate diggers (Executive Office of Energy and Environmental Affairs, 2010).

DMF Enhancement Sites
Figure 4: MA Division of Marine Fisheries shellfish enhancement sites (DMF)

In addition to the enhancement activities conducted by the state, The Massachusetts Oyster Project has grown American oysters at Malibu Beach in Dorchester and is currently growing American oysters at the mouth of the Charles River. These projects were instituted to address water quality issues, but the oysters are not suitable for human consumption.

For restoration and enhancement activities aimed at improving ecosystem services (such as water quality, water clarity, and food provisioning) some site selection criteria for seeding beds might include:

  • Historically productive locations
  • Appropriate bottom conditions
  • Locations that are "sinks" for larvae
  • Areas with sufficient current velocity to bring in food and remove waste
  • Areas without likely threats to shellfish
  • Waters that are well oxygenated
  • Small sub-estuaries that will allow for the scientific assessment of shellfish impacts to water quality and clarity
  • Places that avoid conflict with other potentially disruptive uses (such as shellfish harvesting or boat mooring
  • Areas where restoration investments will likely continue

More specific criteria can be applied once the species have been identified for a restoration or enhancement project. For example, soft-shell clams need to be located in areas protected against waves and boat wakes, and they prefer sandy sediment to sediments of silt and clay.

In Boston Harbor, regulatory criteria also exist for the seeding or re-seeding of shellfish beds. For example, the Massachusetts Division of Marine Fisheries' Draft Shellfish Planting Guidelines prohibit shellfish planting in areas classified as "Prohibited" or "Restricted" unless projects are (1) overseen or conducted by DMF as mitigation for losses to existing shellfish; (2) conducted by DMF or a municipality in Restricted or Conditionally Restricted areas for the purpose of supporting depuration fisheries; or (3) if projects in contaminated areas are used by municipalities as nursery areas for seed shellfish that will be transplanted to Approved or Conditionally Approved waters. Additional criteria exist depending on the purpose of the project, the location of the project, and the proponents of the project (Hickey, et al., 2011). The Guidelines are undergoing review and should be available in early 2012.

While seeding areas and growing shellfish seem to be the most direct ways to restore shellfish beds, measures have also been identified to reduce threats to beds. For example, in 2001, the Town of Weymouth applied for funds to control and abate stormwater draining into the Back River Area of Critical Environmental Concern (ACEC) (The Cecil Group, 2001). The stormwater was believed to be a source of pollutants impacting shellfish resources in the area. More recently, efforts to restore tidal flow at the Trustees of Reservations' World's End property are anticipated to help restore shellfish beds that had declined due to a lack of adequate water flow. Efforts to enforce existing no wake zones can also help reduce over-wash in intertidal areas, thereby (1) minimizing the number of young soft-shell clams washed out of the substrate, and (2) reducing the disruption of sediment in the vicinity of shellfish beds.

These more indirect, stressor-based approaches to shellfish bed protection and enhancement can significantly affect a bed's ability to thrive. In fact, some argue that seeding or re-seeding an area should only be done if stressors have already been reduced to a point where they will not impact the success of the project.

In addition to reducing stressors, harvesting and transplanting shellfish prior to a harmful activity (e.g. dredging) can help ensure that the shellfish beds are not lost. Likewise, the strategic placement of properly cleaned and treated shells (and valves) from restaurants and seafood processors can not only help mitigate the impacts of ocean acidification, but can also create habitat and provide cover against predation.

Literature Cited

Ackerman, S.D., Butman, B., Barnhardt, W.A., Danforth, W.W., and Crocker, J. (2006). High Resolution Geologic Mapping of the Inner Continental Shelf: Boston Harbor and Approaches, Massachusetts. U.S. Geological Survey Open-File Report 2006-1008. Available online at: (Last visited 11/22/2011).

Associated Press. June 13, 2008. Red tide forces closure of Boston Harbor shellfish beds. Avaialble online at:
of_Boston_Harbor_shellfish_beds/srvc=home&position=recent (Last visited 11/21/2011).

Bettencourt, G. (2011). Boston Harbor Softshell Clam Enhancement. Personal Communication.

Boston Society of Natural History. (1892). Proceedings of the Boston Society of Natural History. Vol. 25. P. 315.

Brumbaugh, R.D., M.W. Beck, L. D. Coen, L.Craig and P. Hicks. 2006. A Practitioners' Guide to the Design and Monitoring of Shellfish Restoration Projects: An Ecosystem Services Approach. The Nature Conservancy, Arlington, VA. Available online at: (Last visited 11/21/2011).

Donovan, A. and Tyrrell, M. 2005. From Dune to Shining Sea: The Coastal and Marine Habitats of Massachusetts. Coastlines: Winter 2004-2005. Massachusetts Office of Coastal Zone Management. Available online at: (last viewed 11/14/2011).

Gallagher, E.D., Keay, K.E. (1998). Organism-Sediment-Contaminant Interactions in Boston Harbor. Available online at: (last visited 11/21/2011.

Hickey, J.M., Kennedy, J., Ford, K. (2011). Draft Shellfish Planting Guidelines. Available online at: (Last visited 11/21/2011).

Hill, K. (2004). Mercenaria mercenaria. Available online at: (Last visited 11/21/2011).

Leavitt, D., Burt, B., Murphy, D., and Reitsma, J. Our Current State of Knowledge about razor clam culture in the northeast. Available online at: (last visited 11/21/2011).

Lorio, W.J., Malone, S. (1995). Biology and Culture of the Northern Quahog Clam. SRAC Publication No. 433. Available online at: (Last visited 11/21/2011).

Massachusetts Division of Marine Fisheries. (2011). MA DMF Enhancement Sites (GIS Layer).

Massachusetts Division of Marine Fisheries. (2011). Shellfish Suitability Layers. Available at: (Last visited 11/21/2011).

Massachusetts Division of Marine Fisheries. (2009). Designated Shellfish Growing Areas. Available at: (Last visited 11/21/2011).

Massachusetts Division of Marine Fisheries. Shellfish Sanitation and Management. Available online at: (Last visited 11/21/2011).

Newell, R.I.E. 1989. Species profiles: life histories and environmental requirements of coastal fishes and invertebrates (North and Mid-Atlantic)--blue mussel. U.S. Fish. Wildl. Serv. Biol. Rep. 82(11. 102 ). U.S. Army Corps of Engineers, TR El-82-4. 25 pp.

Newell, C.R., and H. Hidu. (1986). Species profiles: life histories and environmental requirements of coastal fishes and invertebrates (North Atlantic) –softshell clam. U.S. Fish Wildl. Serv. Biol. Rep. 82(11.53). U.S. Army Corps of Engineers, TR EL-82-4. 17 pp.

Executive Office of Energy and Environmental Affairs. (2010) Patrick-Murray Administration Announces Reopening of Hull Shellfish Bad: Bed reopens after three-year project, part of a Boston Harbor shellfish restoration effort. Available online at: (last visited 11/21/2011).

Sellers, M.A., and J. G. Stanley. 1984. Species profiles: life histories and environmental requirements of coastal fishes and invertebrates (North Atlantic) -- American oyster. U.S. Fish Wildl. Serv. FWS/OBS-82/11.23. U.S. Army Corps of Engineers, TR EL-82-4. 15 pp.

Shields, T. Shellfish Stock Enhancement Project. Available online at:
stock_enhancement.pdf (Last visited 11/21/2011).

The Cecil Group, Inc. (2001). Town of Weymouth Master Plan Report. Available online at: (Last visited 11/21/2011).

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Boston Harbor Habitat Atlas
Updated 12/31/2011