Overview | Bacteria | Phosphorus | Other Contaminants

Bacteria Pollution in the Mystic

One of the leading pollutants in our water is bacteria, single-celled organisms that are neither plants nor animals.


Of course, bacteria are everywhere, and most of them are harmless.  The bacteria that we are concerned about in our rivers are pathogens--organisms that cause disease.  

The bacteria that are tested for in water quality testing are actually indicator species--signals of a pollution source that may include many other contaminants. Bacteria we test for are E. coli and Enterococcus, species of bacteria relatively easy to detect. They are a signal of the presence of other bacteria and viruses that could be harmful.   So, where do these pollutants come from?

The pathogens water quality managers focus on come from feces.  (Yes!)

So, how does fecal waste get in rivers and streams in quantities that could affect public health?   

The main source is raw sewage from our sewer lines making its way into our waterways.   (Another source is pet waste; see below.)

Thankfully, our streets no longer look like those of 15th century France or England, before sewer systems were developed, when keeping raw sewage out of streets and water bodies was an impossibility. That’s just where it was dumped.

La Bievre, France, channel built 16th century Photo credit: David Pinkney

La Bievre, France, channel built 16th century Photo credit: David Pinkney

However, raw, untreated sewage entering our water is still a major source of water pollution. Sewage carries bacteria, viruses, protozoa, and parasites, along with anything else flushed down the drain. Contact with these contaminants can lead to diseases ranging from mild gastroenteritis (the stomach flu) to severe water-borne illnesses such as cholera and dysentery. People may come into contact with contaminated water through direct contact in residential areas, water-related activities such as canoeing or swimming.

How is raw sewage getting into our water?

The main pathway for sewage contamination of water bodies is through the stormwater network.  

Now, in an ideal world, stormwater pipes would not have sewage in them.  But there are a number of ways that raw sewage travels from from sewer pipes into stormwater pipes.  The result is that water contaminated from bacteria comes out of stormwater outfalls into streams. The impact on stream water quality can be see in the water quality report card we issue every year with EPA.   

But we also have evidence directly from the stormwater pipes themselves.  For several years, our organization had a “hotspot” monitoring program that tested the water coming out of stormwater outfalls (the ends of pipe networks) in rain storms, in collaboration with US EPA. We reported the results to EPA and to municipalities with the goal of providing additional information in the hard project of tracking down bacteria sources.

Many pipes had frequent significant levels of bacteria, indicating a problem upstream in the stormwater pipe network that leads to them.    

How does the pollution get in the pipes?

There are a few mechanisms that allow wastewater contamination into stormwater systems: 1) illicit connections, 2) leaky and broken pipes, 3) combined sewer systems, and 4) sanitary sewer overflows.

Illicit Connections

An illicit connection is when a storm drain is illegally or unknowingly connected to a storm drain. For example, if a sink, toilet, or laundry machine is connected not to the sewer system but the stormwater system, then sewage and other contaminants make their way directly into our rivers, lakes, streams, and ponds.  These illicit connections get buried and then forgotten. They can remain undiscovered for decades.

Old Infrastructure

Cracks in old stormwater and sewer lines can lead to cross contamination -- allowing sewage to make its way from cracked sewer pipes (headed to Deer Island to get treated) to cracked stormwater pipes (headed to the closest water body).  This probably the most widespread chronic cause of wastewater pollution in our waterways. It’s also probably the hardest source to track down and among the costliest to fix.

Image courtesy of Department of Public Works, Anne Arundel County, Maryland

Image courtesy of Department of Public Works, Anne Arundel County, Maryland

Combined Sewer Overflows

Most of the time, wastewater sewer and stormwater pipes are separate systems.  Wastewater is directed to a wastewater treatment plant.  In greater Boston that means mainly the huge wastewater treatment plant run by the Massachusetts Water Resources Authority (MWRA) on Deer Island in Winthrop.  Stormwater from roads and rooftops, on the other hand, is directed through storm drains and pipes to the nearest waterbody.

But in some older areas of urban systems there are combined sewers, where stormwater from streets and wastewater from homes and other buildings are sent in the same pipe to the wastewater treatment plant.   

Photo credit: US Environmental Protection Agency

Photo credit: US Environmental Protection Agency

What happens in combined sewer systems?

In a combined sewer systems, most of the time sewage goes to a sewage treatment plant (Deer Island), along with any stormwater from light rain that the pipe has capacity to carry to the treatment plant.

However, during periods of heavy rainfall or snowmelt, the amount of rain water in a combined sewer system can overwhelm the system. In these cases, the combined sewer systems are designed to overflow--instead of backing up into houses and streets-- and to discharge directly to nearby streams, rivers, or other water bodies.  These pipes emptying into rivers and streams are “combined sewer overflows,” or CSOs. (See top right picture in the diagram above.)

See this video for a helpful animation showing how CSOs respond in dry weather, light rain and heavy rain.

CSOs are a major target of environmental regulation.  Eliminating CSOs has been a major tool in the historic cleanup of Boston Harbor over the past thirty years. Eliminating CSOs on the Mystic, Charles and Neponset Rivers, as well as CSOs that emptied directly into Boston Harbor has helped turn the “dirtiest harbor in America” into what’s been called “a great American jewel.”

But CSOs remain, and continue to be significant sources of pollution.  

Are there CSOs on the Mystic River?

Currently, there are CSOs along the Alewife Brook and the Mystic River as well as the Chelsea River.  Annual discharges from CSOs--although much reduced--are still measured in the millions of gallons. The map shows currently active CSOs and ones that have been eliminated.

The following table shows specific progress in the Mystic.  It shows the volume (in millions of gallons) of CSO discharges in 1992 and 2017, and compares those numbers with the goals announced in the Long Term CSO Control Plan (LTCP), mandated by federal court order.  Much progress has been made since 1992, but these pipes remain significant sources of contamination. Some CSOs have local treatment facilities that treat the water with disinfectant. The final column shows the percentage of total volume that gets this minimal level of treatment before discharge.  

Data source: MWRA

Data source: MWRA

Sewer separation, Chelsea, MA; Image from MyRWA

Sewer separation, Chelsea, MA; Image from MyRWA

What is a Sanitary Sewer Overflow?


While combined sewer overflows were designed and built, sanitary sewer overflows (SSOs) are illegal connections. Like CSOs, they usually happen during heavy rain events when stormwater infiltrates and overloads the sewage system, but can also happen due to improper maintenance or vandalism.


The EPA estimates that there are at least 40,000 SSOs each year across the US. Recurring SSO sites exist throughout the Mystic River Watershed, and usually occur during heavy rains because of stormwater infiltrating and overloading the sewage system. Although these overflows are illegal, they continue to occur.

Is pet waste really a problem?

In 1991 the EPA designated pet waste as a source of pollution, on par with herbicides, pesticides, oil, grease, and toxic chemicals. In addition to e.coli and fecal coliform, which causes cramps, diarrhea, intestinal illness, and even kidney disorders, dog waste can contain giardia, salmonella, and roundworms.

The EPA estimates that two or three days’ worth of droppings from a population of about 100 dogs would contribute enough bacteria to temporarily close a bay, and all watershed areas within 20 miles of it, to swimming and shell fishing.

Luckily, the solution is simple. PICK UP AFTER YOUR PET AND ENCOURAGE OTHERS TO DO SO!