Threats to the Bay

Threats to Cape Cod Bay & Water Quality Parameters


A CTD is deployed to measure temperature, salinity and depth.

A CTD is deployed to measure temperature, salinity and depth.

Over 30 discharge facilities are located in the Cape Cod watershed. While some offer advanced treatment with nutrient removal of their effluent, most are designed for only secondary treatment. The number of discharge facilities in combination with the slightly pervious sandy soil of the Cape is a potential hazard that needs to be closely monitored. Also within the watershed are 90 known facilities that handle hazardous wastes, and 3 facilities with National Pollution Discharge Elimination System (NPDES) permits. Although limitations and monitoring requirements are in place for the effluent at these facilities, a close appraisal of the effects on the surrounding ecosystem is warranted.

Polluted runoff is another major problem on the Cape. 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.

The consequences of pollution have already manifested in the bay. 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 in the bay, better known as eutrophication. Eutrophication has been linked to a number of different harmful processes in coastal waters (e.g., hypoxia, HABs), and there is evidence that eutrophication is already occurring in certain regions of the bay.

Habitat Destruction

One of the most important, yet least studied habitats in Cape Cod Bay are the eelgrass ecosystems. In shallow areas of Cape Cod Bay, eelgrass (Zostera marina) 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 eelgrass ecosystems, eelgrass beds are threatened by a number of anthropogenic perturbations. Declines in seagrass populations have been linked to physical disturbances (i.e., dredging, construction, shellfishing, propeller damage from boating), turbidity (i.e. topsoil runoff, activities that resuspend sediments), and pollution (including eutrophication). In Cape Cod Bay the destruction off eelgrass habitats by each of these mechanisms is evident. Hydraulic pumping by commercial sea clammers and the use of draggers fitted with teeth to pull out quahogs completely uproot the eelgrass plants, requiring years to recover (Neckles 2005). This is compounded by the damage from propellers by the powerboats that concentrate in the eelgrass beds of the Bay for recreational fishing. Adding the additional stress of eutrophication, as discussed previously, makes the health of this already fragile ecosystem even more tenuous.


The consequences of pollution have already manifested in the Bay. 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 in the Bay, better known as eutrophication. Eutrophication has been linked to a number of different harmful processes in coastal waters, and there is evidence that eutrophication is already occurring in certain regions of the Bay. 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 Cape Cod waters. During the spring, Phaeocystis blooms occur frequently. 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). The occurrence of this species was particularly high in Bay waters this summer, and, due to its lifecycle of dormant cysts, is likely to become a repetitive occurrence if conditions remain conducive, i.e. high nutrient input, stratification (Mcgillicuddy et al. 2003). Although there were no documented deaths as a result of the bloom in the Bay this summer, the effects were still felt by the loss of income of commercial fishermen from shellfish bed closures.


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. This had occurred in areas of Chesapeake Bay and the Gulf of Mexico, giving these areas the name “dead zones.” Although hypoxic areas of Cape Cod Bay 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 such as flounder, tautaug, sea bass, and, most notable, striped bass have likewise suffered from overexploitation. In the early days, charter captains could guarantee their customers a catch. Now a common saying is “That’s why they call it fishing and not catching.” The apparent, recent recovery of the striped bass fishery is a result of the close monitoring of this species implemented by the state. Unfortunately, this recovery is a unique case and has not occurred with other commercial species. It is now the poignant prediction of fishermen that the bluefish will be the next population to crash in the Bay.

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 decade, however, it has been re-implemented in an attempt to increase the harvesting of these clams.


Key in this study will be to map out the spatial and temporal variability in nutrient fluxes in the bay, focusing specifically on nitrogen and phosphorous. Excessive nutrient input is behind most major problems affecting coastal ecosystems, (e.g., eutrophication, algal blooms, hypoxia). It is therefore important that we establish baseline data for the bay and continue to closely monitor nutrient levels to address existing and imminent problems.

Chlorophyll a

Chlorophyll a is a green photosynthetic pigment found in most phytoplankton and plant cells. It is a commonly measured parameter of water quality as it can be used as an estimate of the amount of organic matter produced within the bay. By keeping tract of trends in chlorophyll a, we are able to assess effects of nutrients entering the bay and better understand the delicate balance between photosynthetic rates, nutrient inputs, and oxygen levels in our bay waters.

Dissolved Oxygen

Dissolved oxygen concentrations are a measure of how well the water is aerated. This parameter is one of the best and most immediate indicators of a system’s health (EPA). Because oxygen is needed to support animal and plant life, consequences of declining D.O. levels will set in quickly. This immediate impact on plant and animal life makes measuring the level of oxygen an important means of assessing water quality. Additionally, at low oxygen conditions, nutrients (and other pollutants) will be released from sediments thereby exacerbating problems.

Temperature and Salinity

Water temperature and salinity are two of the most important physical properties of the marine environment, influencing many physical (density), chemical (capacity to hold D.O., sensitivity to toxic wastes), and biological processes (metabolic processes, photosynthesis) as well as dictating the types, distribution and abundance of marine flora and fauna. Monitoring levels of these properties, and more importantly, changes in the levels, will provide a direct indication of potential problems.

A Secchi disk is used to measure turbidity (water clarity).

A Secchi disk is used to measure turbidity (water clarity).


Turbidity, a measure of water clarity or how much the material suspended in the water column decreases light penetration, will also be measured as an indicator of the quality of the water in the bay. High levels of turbidity can result from anthropogenic disturbances such as urban runoff, waste discharge, dredging, and boating, as well as natural disturbances such as storms, wave action, and bottom feeding animals. Highly turbid waters are detrimental to the entire ecosystem from sediment quality, to water chemistry, to the survival of plants and animals. Some of the associated negative impacts of high levels of turbidity include lowering the rates of photosynthesis, smothering benthic organisms, and altering bottom material and sediment size.


Ohrel, R.L., & Register, K.M. (2005). Volunteer Estuary Monitoring: A Methods Manual. 2nd Edition. EPA-842-B-06-003. Washington, D.C.: U.S. Environmental Protection Agency, Office of Wetlands, Oceans, and Watersheds to The Ocean Conservancy, pp. 396.

United States Environmental Protection Agency. (2007, February 6). Monitoring and Assessing Water Quality. Retrieved from