Threats to the Bay and Sound

Cape Cod Bay and Nantucket Sound are ecologically rich complexes of coastal and marine habitats. Beaches, wetlands and offshore waters are home to plant and animal communities that include commercially valuable species of finfish and shellfish, marine mammals, sea turtles and birds.

Cape Cod Bay is part of the much larger Gulf of Maine system that contains some of the world’s most productive waters. While strong tides move water around in the Bay, it can take about a month for a full exchange of water to occur. Nantucket Sound is located at a confluence of the cold Gulf of Maine and the warm Gulf Stream. It is protected from the Atlantic Ocean by Martha’s Vineyard and Nantucket Islands, and is shallower than the Bay.

Cape Cod Bay and Nantucket Sound were designated as state ocean sanctuaries more than 40 years ago to “prohibit activities that may significantly alter or endanger the ecology or appearance of the ocean, seabed or subsoil.” This designation recognized the vitality and importance of the Bays and the Sound’s resources to the state.

Threats to Cape Cod Bay and Nantucket Sound waters:


From a distance both Cape Cod Bay and Nantucket Sound appear healthy. However, according to the Cape Cod Commission, Cape Cod has a water problem. The saltwater border that has defined our peninsula is being poisoned by nitrogen. About 80% of the nitrogen that enters Cape Cod’s watersheds is from septic systems. The conditions it creates destroy animal habitat and result in frequent violations of water quality standards indicated in part by fish kills and diminished shellfisheries. The impacts of this pollution need to be closely monitored.

Polluted runoff is another major problem impacting our coastal waters. This type of pollution is a result of contaminants picked up in rainwater and melting snow which are eventually emptied into the bay. Examples of possible pollutants picked up in runoff include fertilizers and other lawn/garden chemicals, wastes from pets, salt from roadways, and oil and gasoline leaked from automobiles. In many towns on the Cape this problem is compounded by the large parking lots located near or directly adjacent to harbors. Not only are the oil and gasoline associated with parked automobiles a problem, but these large parking lots are often the site of the disposal of snow (and the associated salt used to treat the roads) cleared from roads during the winter.

Habitat Destruction

One of the most important, yet least studied habitats in our coastal waters are the eelgrass ecosystems. Eelgrass (Zostera marina) in Nantucket Sound is found predominately in the nearshore waters from Monomoy west to Hyannisport and the shore of Falmouth. It is found more extensively in shallow areas of Cape Cod Bay, along most of the shoreline and out on Billingsgate Shoal. In both the Bay and the Sound, eelgrass is fundamental in structuring the resident flora and fauna. Eelgrass systems are highly productive and extremely important biologically. They act as a refuge and nursery for juvenile fish and shellfish, many of which are commercially important species in this region and typically support a higher diversity and abundance of marine life compared to surrounding unvegetated areas (Heck et al. 1989). Seagrasses are equally important from a purely physical perspective in that they help to prevent erosion by stabilizing sediments with their extensive root systems as well as aid in filtering contaminants from the water column.

Despite the obvious value of seagrass ecosystems, eelgrass beds in the Bay and the Sound are threatened by a number of anthropogenic perturbations. Declines in eelgrass habitat have been linked to physical disturbances (i.e., dredging, construction, shellfishing, propeller damage from boating), turbidity (i.e. topsoil runoff, activities that re-suspend sediments), and pollution (including eutrophication). There is evidence of the destruction off eelgrass habitats in the Bay and the Sound by all of these mechanisms making the health of this already fragile ecosystem even more tenuous.


The consequences of pollution have already manifested in our coastal waters. In addition to the direct, toxic effects of pollution, excessive nutrient input from both point and nonpoint sources leads to high levels of plant growth. This process, known as eutrophication, is occurring to some degree in Cape Cod Bay and Nantucket Sound and more noticeably in the coastal ponds and embayments that discharge into them. Eutrophication has been linked to a number of different harmful processes in coastal waters. Two symptoms of eutrophication that have been extensively documented are harmful algal blooms (HABs) and hypoxia.

Harmful Algal Blooms (HABs)

Algal blooms occur primarily during the spring and summer in our coastal waters. During the spring, Phaeocystis blooms occur frequently in Cape Cod Bay. The negative impacts of a bloom of this phytoplankton are far reaching, affecting the entire food chain by out-competing other beneficial species of phytoplankton (Roberts 2003, Tang 2003), affecting zooplankton growth and production (Tang 2001, Turner et al. 2002), and being a nuisance to feeding right whales (Kelly et al. 1998). A more well-known species of phytoplankton resulting in HABs is Alexandrium sp., one of the species behind the phenomenon of red tides. Red tides have been linked to the deaths of fish, whales, and humans (Anderson 1994, Bushaw-Neston & Sellner 1999). Blooms of this species vary greatly from year to year.  Due to its lifecycle of dormant cysts, Alexandrium blooms are likely to become a repetitive occurrence if conditions remain conducive, i.e. high nutrient input, stratification (Mcgillicuddy et al. 2003). Although there have been no documented deaths as a result of the recent blooms that have occurred in the Bay or the Sound, the effects are still felt by the loss of income of commercial fishermen from shellfish bed closures and impacts on conch fisheries.


Closer inshore, the negative impacts of pollution are evident in the sediments. Sediments in and around harbors such as Rock Harbor and Wellfleet Harbor, which were once sandy, are now composed primarily of a silty, dark mud. If disturbed, these sediments release a distinct sulfurous odor indicative of areas of low oxygen. This odor comes from the production of hydrogen sulfide by bacteria which reside in low oxygen (hypoxic) sediments. Since most organisms are stressed by low oxygen levels, hypoxic waters are usually devoid of most life. While motile organisms such as fish can leave these areas, benthic organisms will be killed. Portions of the estuaries discharging into Nantucket Sound, for example the Three Bays complex in Barnstable, also have oxygen-depleted sediments. This had occurred in areas of Chesapeake Bay and the Gulf of Mexico, giving these areas the name ‘dead zones’. Although areas of low oxygen in the coastal waters of Cape Cod are not nearly as extensive as observed in these locations, these areas need to be monitored and remedied before the problem progresses.


This region of Massachusetts was given the name of Cape Cod because of its abundance of codfish. Today these fish have virtually disappeared from the waters of the Bay. Other species found in the Bay and Sound, such as flounder, tautaug, sea bass, and striped bass have likewise suffered from overexploitation.

With reference to some commercial shellfish species, overexploitation is tied directly to habitat destruction. The development of different methods of fishing to increase the catch of a declining stock has been disruptive. Hydraulic pumping for sea clams was once outlawed in the Bay. Over the past several decades, however, it has been re-implemented in an attempt to increase the harvesting of these clams.


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