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Boston Harbor and Massachusetts Bay
Massachusetts Water Resources Authority



Alexandrium: Alexandrium tamarense typically may bloom during April to June and can cause paralytic shellfish poisoning, known as PSP or red tide; it has been periodically found in Massachusetts since the 1970s. Toxicity is generally not found in shellfish until much higher cell counts are seen in the overlying waters. To calculate the threshold we determine the maximum number of total Alexandrium cells (Alexandrium tamarense plus unidentified Alexandrium spp.) seen in any nearfield sample. (See also: Red Tide)

Aquifer: A geologic formation that holds groundwater. Many non-MWRA communities rely on wells drilled into aquifers for their drinking water supplies.

Bacteria:See Enterococcus and Fecal Coliform

Benthic Diversity Thresholds: One way to track the status of a marine ecosystem is to measure the diversity of the organisms in the communities that comprise the ecosystem, such as the soft-sediment communities (benthic infauna) in the sediment. The benthic diversity thresholds are intended to indicate whether there is a change from baseline conditions (either toward more or less diversity) now that the outfall is discharging. Of the dozens of statistical measures of diversity that have been developed by researchers over the past few decades, four are tracked within the MWRA monitoring program to show possible changes in diversity.

Two of these indices, total number of species per sample and Fisher's log-series alpha, are measures of species richness (how many species are present). Both measures track species richness while total species per sample is easy to describe to a general audience, Fisher's Log-series alpha has a theoretical grounding favored by some researchers. The other two diversity indices tracked by MWRA's monitoring are among those most commonly used by ecologists in many environments. Pielou's J' is a measure of how evenly individuals are distributed among species in a community. Samples where most species have about the same number of individuals have high evenness, while samples where most of the individuals belong to one or a few species have low evenness. Finally, Shannon-Wiener H' is a diversity measure that is sensitive both to species richness and to species evenness in a community.

The extreme winter storms of December 1992 caused 24-foot seas in the vicinity of the outfall, moving sediments and burying some areas under inches of sand, mud, or gravel even though the ocean is about 100 feet deep in the area. This physical disturbance was at least partially the cause of the decline seen in the two richness indices between 1992 and 1993. The communities recovered rapidly, and by the late 1990s appeared to be showing a several-year cycle in species richness (data from farfield stations also show this apparent trend).

Bioaccumulation: The process by which toxic chemicals can accumulate in animal tissues and become concentrated when they move up the food chain.

Biochemical Oxygen Demand (BOD): BOD is used as a measure of the quantity of oxygen consumed by microorganisms during the decomposition of organic matter. Bacteria and fungi use oxygen as they break down vegetation into carbon dioxide, water, phosphate and nitrate. As oxygen is consumed, the level of dissolved oxygen in the stream begins to decrease.

BOD is typically divided into two parts- carbonaceous oxygen demand and nitrogenous oxygen demand. Carbonaceous biochemical oxygen demand (CBOD) is the result of the breakdown of organic molecules such a cellulose and sugars into carbon dioxide and water. The BOD test measures the oxygen demand of biodegradable pollutants whereas the COD test measures the oxygen demand of biogradable pollutants plus the oxygen demand of non-biodegradable oxidizable pollutants.

Organisms such as plants and algae produce oxygen when there is a sufficient light source. During times of insufficient light, these organisms consume oxygen. When the dissolved oxygen is too low, aquatic life intolerant of low oxygen levels become stressed. Eventually, species sensitive to low dissolved oxygen levels are replaced by species that are more tolerant of adverse conditions, significantly reducing the diversity of aquatic life.

Boston Harbor Project: The Boston Harbor Project gradually reduced treatment plant discharges to the Harbor.

In 1985, a federal court order set an ambitious schedule for the newly formed MWRA to plan and construct new sewage treatment facilities. These facilities would end the discharge of untreated and partially treated sewage to Boston Harbor. The so-called "Boston Harbor Project" helped the water, sediments, and living natural communities in Boston Harbor recover from centuries of receiving Greater Boston’s sewage. This undertaking included four major construction projects:

1. Facilities at the Fore River shipyard in Quincy to process sewage sludge into commercial fertilizer pellets, ending the discharge of sludge into the harbor.

2. A new secondary wastewater treatment facility, the new Deer Island Treatment Plant (DITP), to replace the failing and undersized primary treatment plants at Deer Island and Nut Island (NITP).

3. A tunnel from Nut Island to DITP to transport South System sewage to DITP for secondary treatment, enabling flows from throughout MWRA’s service area to receive secondary treatment and greatly lessening pollution to the harbor.

4. An outfall-diffuser system to discharge treated effluent 9.5 miles offshore into Massachusetts Bay, increasing dilution and minimizing potential environmental impacts in the bay.

In addition to taking on these major construction projects, MWRA has addressed the problem of combined sewer overflows (CSOs), which discharge a mixture of stormwater runoff and sewage directly into the harbor during heavy rainstorms. In the 1980s, 88 CSOs in the harbor and its tributary rivers discharged an estimated 3.3 billion gallons of partially treated or raw combined sewage annually. MWRA's CSO Control Plan includes the closing of many CSOs and the addition of treatment to others.

Chlorination: Disinfection by adding the chemical chlorine, the active ingredient in household bleach. Chlorine is very effective at killing pathogens but is also poisonous to other organisms at high enough concentrations.

Chlorophyll: Chlorophyll is a measure of the amount of microscopic plants (phytoplankton or algae) in the water. In Massachusetts Bay, production of algae is the basis of the food web. However, excessive growth of algae can lead to undesirable consequences, such as oxygen depletion at depth due to decomposition of organic matter. Effluent from the outfall is rich in nutrients, and therefore could potentially cause excessive algal growth.

Chlorophyll Thresholds: There are annual and seasonal chlorophyll thresholds for the "nearfield," the group of stations within about three miles from the outfall that are most likely to be affected by nutrient-rich effluent. Because the levels of chlorophyll in the water naturally vary over the year, there are separate thresholds for different seasons. In most years, Massachusetts Bay experiences a "spring bloom" characterized by high chlorophyll levels as lengthening days provide enough sunlight for algae to grow quickly. Chlorophyll typically drops in summer, as the nutrients in well-lit surface waters are used up. When the weather cools, the surface and bottom waters mix, which usually gives rise to a "fall bloom" as nutrient-rich bottom waters are mixed up into the well-lit surface layers. As the days become short, chlorophyll levels drop again since there is not enough light for algae to grow.

Clarity: Water clarity in the harbor and the rivers is primarily affected by concentrations of algae and suspended solids. Secchi disks are a simple way to approximate the transparency of water. White or black-and-white disks are lowered into the water and the maximum depth at which they are visible is recorded. Large secchi disk depths indicate good water clarity. Secchi disk depths less than 1.8 meters indicate poor water clarity.

Combined Sewer Systems and Combined Sewer Overflows:
Some communities have antiquated combined systems that carry sewage and stormwater runoff from homes and businesses in the same pipes. These systems were designed to overflow when the volume of flow is more than the pipe can carry, causing mixed stormwater and sewage discharges from outfall pipes into Boston Harbor and its tributary rivers during wet weather. Both an overflow structure and an overflow event can be referred to as a Combined Sewer Overflow (CSO). Learn more about CSOs at

Sanitary Sewer Overflows
Sanitary (not combined) sewer systems are not designed to carry stormwater runoff. Heavy rains leaking into sewer pipes can cause these systems to overflow into a stream or other body of water.

Drainage systems collect rainwater runoff from streets and channel it to a nearby river or harbor. Unfortunately, storm drainage is frequently
contaminated with sewage from leaking pipes or illegal sewer connections from buildings. Animal waste on the streets also contaminates stormwater, as does car exhaust, street dirt, and litter.

CSO Treatment Facility: A treatment facility that operates in wet weather to treat combined sewage before discharge. Includes disinfection; may also include some removal of suspended solids or floatable pollutants.

Dechlorination: The addition of a chemical (usually sodium bisulfate or sodium thiosulfate) to neutralize the toxicity of chlorine after it has been used for disinfection.

Disinfection: Untreated sewage carries large numbers of potentially disease-causing pathogens originating in human waste that would be a health hazard if discharged into recreational or shellfishing areas. Llike most wastewater treatment plants, Deer island uses a form of chlorine (sodium hypochlorite, the active ingreadient in bleach) to disinfect wastewater before discharging. Unfortunately, sodium hypochlorite is toxic not only to microbes but also, in high enough concentrations, to aquatic life.

Dissolved Oxygen (DO): Fish and other aquatic animals breathe oxygen dissolved in the water. Algae and other plants growing in the water produce oxygen, and atmospheric oxygen also dissolves in water at the surface. In polluted ecosystems dissolved oxygen can fall below levels necessary to sustain

Dissolved Oxygen Depletion Rate: Even if dissolved oxygen concentrations remain healthy, an excessively rapid rate of decrease could signal a future problem. A low rate indicates DO dropped only slowly. The threshold for DO depletion rate is based on a change from the baseline; the caution threshold is a rate faster than 1.5 times the baseline mean rate, while the warning threshold is twice the baseline mean rate.

Dissolved Oxygen Thresholds:The concentration of dissolved oxygen (DO) in the water indicates the balance between production by algae and consumption by aquatic organisms and the decomposition of organic matter. Excessive organic matter may result in oxygen depletion, which may in turn adversely affect the aquatic ecosystem. The amount of oxygen that the water can hold is related to water temperature, salinity, and pressure; thus, the percent saturation of dissolved oxygen is a measure that takes these factors into account. Monitoring locations for which there are DO thresholds include the "nearfield," the group of stations within about three miles from the outfall, and "Stellwagen Basin," a deep area nine miles east of the outfall. DO thresholds apply to the part of the year when the water column is stratified, i.e. from June - October.

Dissolved oxygen concentration and percent saturation naturally fell below 6 mg/l on occasion during the baseline period. The state standard, on which the thresholds were based, allows an exception to numerical thresholds if background conditions are lower, as is the case here; thus, the threshold is not exceeded unless the value falls below the threshold and below background.

Effluent: Disinfected wastewater, the final liquid by-product of the wastewater treatment process flowing out of a treatment plant.

Enterococcus: Enterococcus is a type of bacteria present in the intestines of warm-blooded animals and is considered to be an excellent indicator of human sewage. During the swimming season, a geometric mean count above 35 colonies per 100 mL (an average of counts from samples collected over several days or weeks) results in prolonged closure of a swimming area.

Estuary: A water body where salt and fresh water mix. Examples are Boston Harbor, Plum Island Sound, and Narragansett Bay.

Eutrophication: In marine environments, an overabundance of organic material and of nutrients, especially nitrogen, can lead to a condition called eutrophication, or over-enrichment of the system. Symptoms of eutrophication can include blooms of nuisance phytoplankton, discoloration of the water, bad odors, depression of dissolved oxygen in the water and sediment, shading out of seagrasses, and reduction of biodiversity in bottom-dwelling animal communities.

Farfield: The farfield sampling stations are greater than 7 kilometers (4 miles) from the outfall diffuser. Locations are in Boston Harbor, Massachusetts Bay, Cape Cod Bay, and the Stellwagen Bank National Marine Sanctuary to assess any changes that may be occurring farther away from the outfall discharge.

Fecal Coliform: Because most pathogens are very difficult to measure directly, their presence is usually inferred from the presence of fecal coliform bacteria which are also found in human and animal waste but are easier to measure. If counts of fecal coliform above state standards are measured by a monitoring agency, beaches are posted as unsafe or shellfish beds are closed until levels fall back down.

Groundwater: Water that saturates the rocks and soil. It flows through the ground and, if it is contaminated, can carry pollutants into surface water bodies.

Halocline: See Pycnocline

Headworks: Preliminary sewage treatment facilities that remove grit and large objects from the sewage flow before it enters MWRA treatment plants. First stage of primary treatment.

Infiltration & Inflow (I/I): Infiltration is the seeping of groundwater into leaky pipes during wet weather. This is a large, unwanted source of water to sewers. Inflow is the illegal discharge of stormwater to sanitary (uncombined) sewers, sump pumps, roof drains, and basement and foundation drains from homes directly to sewers instead of to drainage systems. This inflow adds large volumes of stormwater to already overtaxed sewer systems.

Interceptors: Large regional sewers that collect sewage from local sewerage systems.

Nearfield: The nearfield sampling stations are within about 7 kilometers (4 miles) of the outfall diffuser, to monitor any changes occurring near the discharge.

Nonpoint Sources: Pollution sources at many unspecified locations, such as unsewered rainfall runoff, leaking septic systems, and other intermittent sources of pollution.

Nuisance Algae Thresholds: Nuisance algal blooms are less predictable than the normal, beneficial algal blooms that produce oxygen and food for marine life; some nuisance blooms did occur during the baseline monitoring period. There is public concern that effluent nutrients could feed a red tide bloom in the vicinity of the new outfall, or otherwise increase the abundance of nuisance algae. Therefore, the Contingency Plan has thresholds for abundance of Alexandrium, Phaeocystis pouchetii, and Pseudonitzschia, which are triggered if the abundance of any of these becomes unusually high.

Nutrients such as nitrogen and phosphorous are necessary for the growth of plants, but excess nutrients can accelerate the growth of algae or aquatic weeds. In marine waters the limiting nutrient is nitrogen, so that adding nitrogen increases algae. In fresh water, the limiting nutrient is usually phosphorus. Many detergent manufacturers have eliminated phosphates from their products in order to avoid causing nutrients pollution of freshwater lakes and streams.

Opportunistic Benthic Organisms: The presence of pollution-tolerant or opportunistic species is another measure of possible pollution impact on sediments in the vicinity of the outfall. These are species that can build up to high population levels in response to, for example, increased deposition of organic matter. In their selection of an outfall location in 1988, EPA modeled the deposition of organic matter and determined that with a secondary discharge, impacts would be minimal.

Based on a review of the species found in Boston Harbor, Massachusetts Bay, and Cape Cod Bay sediments during baseline sampling, several species have been identified as opportunists: Capitella spp. and Capitella capitata complex, Polydora cornuta, Streblospio benedicti, Ampelisca abdita, Ampelisca vadorum, Ampelisca macrocephala, and Mulinia lateralis. The Ampelisca species were included in the list because they are tolerant to moderate levels of organic enrichment, even though they cannot tolerate high levels. For example, the appearance of large populations of Ampelisca in Harbor sediments in the mid-1990s was one of the early signals of the Harbor's recovery.

The Contingency Plan thresholds for percent opportunists were set well below levels seen in Boston Harbor throughout the 1990s.

Outfall: Pipe releasing wastewater at a fixed location. Often outfalls are placed away from shorelines in areas where the wastewater will be rapidly diluted.

Oxygen-consuming Organic Matter: If a large amount of organic material--leaves, plants, wastewater or plant growth spurred by excess nutrients--decomposes in a body of water, it depletes the dissolved oxygen level necessary to support aquatic life.

Pathogens: Short for "pathogenic microorganisms," these disease-causing viruses and bacteria enter the harbor through inadequately treated or raw sewage and from animal and bird waste in storm runoff. They can cause stomach ailments, ear, eye, or skin infections, and even serious diseases such as hepatitis.

PAHs -- polycyclic aromatic hydrocarbons. PAHs are a group of chemicals that are formed during the incomplete burning of coal, oil, gas, wood, garbage, or other organic substances, such as tobacco and charbroiled meat. There are more than 100 different PAHs. They can also be found in substances such as crude oil, coal, coal tar pitch, creosote, and roofing tar. They are found throughout the environment in the air, water, and soil. They can occur in the air, either attached to dust particles or as solids in soil or sediment.  Studies of people show that individuals exposed by breathing or skin contact for long periods to mixtures that contain PAHs and other compounds can also develop cancer.

PCBs -- polychlorinated biphenyls are synthetic organic chemicals comprising 209 individual chlorinated biphenyl compounds (known as congeners). Exposure to each of these compounds is associated with different levels of risk for harmful effects. There are no known natural sources of PCBs. Although PCBs are no longer manufactured in the United States, there are ways people can still be exposed to them, including eating contaminated seafood.

pH: pH is a measure of the alkalinity or acidity of the effluent. Small fluctuations in pH do not have an adverse effect on marine environments, because seawater is well buffered. Secondary treatment technology at Deer Island tends to produce effluent at the low end of the range.

Phaeocystis: Phaeocystis pouchetii, one of several species of so-called "nuisance algae," usually blooms during February to April but can bloom at any time. The species is not toxic, but individual cells can aggregate in gelatinous colonies that may be poor food for zooplankton. MWRA monitors Phaeocystis in its outfall ambient monitoring program. Reporting on seasonal abundances of Phaeocystis near the outfall is part of the Contingency Plan. Adverse aesthetic or other impacts from Phaeocystis blooms could include persistent foam on the sea surface and/or unpleasant, acrid odors reminiscent of burning plastic. For information on Phaeocystis exceedances, see the Contingency Plan Exceedances page.

Pseudonitzschia: Pseudonitzschia multiseries blooms can occur during November to March and produce domoic acid, which can cause a condition known as amnesic shellfish poisoning. To calculate the threshold we calculate the nearfield average count of algae in a group that includes the toxic species Pseudonitzschia multiseries, the closely related Pseudonitzschia pungens, and any unidentified Pseudonitzschia species.

Pycnocline: A horizontal layer or depth range of changing density in the water. The word "pycnocline" stems from the Greek word "puknos" , meaning "thick" , and "-cline" means "gradual change" or "gradient". Because density varies with temperature and salinity, a pycnocline encompasses a layer of changing temperature (thermocline) and changing salinity (halocline). When surface water has higher temperature its density is lower, creating stratification, or layering of the water (see graphic).

Adapted from a graphic from the website of the University of Hawaii at Manoa

Understanding stratification is important in measuring the effects of wastewater discharges into Massachusetts Bay. A pycnocline is present in Massachusetts Bay from about May through October, when winds are weaker and surface waters heat up due to more plentiful sunshine; typically the pycnocline is up to 10 meters (33 feet) thick, and occurs at about 10-30 meters below the surface. During the unstratified winter months, there is no pycnocline and effluent from the MWRA outfall on the seafloor tends to mix upward to the water surface, while during stratified conditions the rest of the year it tends to remain deeper than the pycnocline.

Red Tide: The term "red tide" most often refers to Alexandrium tamarense, one of several harmful phytoplankton species. Alexandrium tamarense typically may bloom during April to June and can cause paralytic shellfish poisoning, known as PSP; it has been periodically found in Massachusetts since the 1970s. For more information go to

Runoff: Rainfall or snowmelt moving over and through the ground. As the runoff moves, it carries away natural and human-made pollutants, depositing them into lakes, rivers, wetlands, coastal waters, and underground water sources. Runoff can carry bacteria and nutrients from livestock, pet wastes, and faulty septicsystems; fertilizers, herbicides, and pesticides from agricultural and residential areas; and oil, grease, and toxic chemicals from automobiles and other sources.

Sanitary Sewers: A sewerage system that carries wastewater only from the drains and toilets of homes and businesses.

Sanitary Sewer Overflows: These overflows occur when the capacity of a sewer system is overwhelmed and the sewer "backs up," spilling untreated wastewater into nearby waterways.

Secondary Treatment: The second stage of the wastewater treatment process, often using microorganisms to break down oxygen-consuming organic matter in wastewater.

Sediment Contamination: Sediments tell us the history of pollutant inputs because, over time, sediments accumulate toxic contaminants. Contaminants stick to particles, which settle to the bottom. Concentrations of toxic organic compounds and most heavy metals in the water in Boston Harbor meet state standards; there are very few measurements of toxic chemicals in the freshwater portions of the harbor's tributaries, however. Even if water quality standards are met, toxic chemicals can accumulate in animal tissues or in bottom sediments to levels that harm marine life.

Sediment Enrichment: Even if the water's dissolved oxygen does not fall too low, a lot of organic matter falling on the bottom produces an organic-rich sediment. Bacteria in the sediment use up oxygen as they consume the organic matter. While healthy sediments have an oxygenated layer above a layer that is anaerobic (without oxygen), very organic-rich sediments have no oxygenated layer. In this environment, anaerobic bacteria can thrive (as they use sulfur instead of oxygen), and produce toxic hydrogen sulfide. Few animals can live in this oxygen-poor, sulfide-rich environment; the resulting low diversity and small number of animals indicate an unhealthy ecosystem.

Sediment Oxygen Demand: Bacteria and other organisms metabolize organic matter, depleting oxygen. If the sediments use up oxygen too quickly, it can mean that they are polluted by excess organic matter.

Sludge: The solids which settle out during the sewage treatment process. Sludge from the Deer Island Treatment Plant was discharged into Boston Harbor until 1991. More Info.

Stormwater: Rainwater and snow melt that runs off the land. In developed areas, stormwater is collected by a system of storm drains.

Surfactants: Chemical compounds, such as those found in detergents, that break down grease and other kinds of dirt. They are toxic to aquatic life in high concentrations.

Stratification: See Pycnocline

Suspended Solids: Tiny particles of material, like mud, sand, and organic debris, that are suspended in water but can settle out over time. Pollutants often attach to solids or are solids themselves (e.g. pathogens, toxic contaminants, and some nutrients). Excess suspended solids can clog the feeding organs of some animals and prevent light from reaching aquatic plants. See also Total Suspended Solids.

Thermocline: See Pycnocline

Toxic Chemicals: Also called toxic compounds, these chemicals are poisonous at high enough concentrations. They include toxic organic compounds such as hydrocarbons, PCBs, and pesticides. Heavy metals can also be toxic at high concentrations, and include arsenic, cadmium, chromium, copper, lead, mercury, molybdenum, nickel, silver, and zinc.

Toxicity: The capability of a substance to poison living creatures. Some of the substances found in wastewater that can cause toxicity in water or sediments include chlorine, surfactants, heavy metals, and some organic compounds.

Tributary: A stream draining into another stream or river, pond, lake, or estuary.

Water Quality Standards (see table):

Inland Water Class B:  These waters are designated as a habitat for fish, other aquatic life, and wildlife, and for primary and secondary contact recreation.  Where designated they shall be suitable as a source of water supply with appropriate treatment.  They shall be suitable for irrigation and other agricultural uses and for compatible industrial cooling and process uses.  These waters shall have consistently good aesthetic value.

Coastal and Marine Class SB:  These waters are designated as a habitat for fish, other aquatic life, and wildlife, and for primary and secondary contact recreation.  In approved areas they shall be suitable for shellfish harvesting with depuration (Restricted Shellfishing Areas).  These waters shall have consistently good aesthetic value.

Watershed: geographic area in which water, sediments, and dissolved materials drain to a common outlet—a point on a river or lake, an estuary (like Boston Harbor), or an ocean.