The Merrimack River Watershed Council released its annual report this week in which it revealed the results of a year's worth of water quality testing at 20 locations in the river from Lowell to Newburyport.

What the organization expected to find from the testing was that during heavy rain, untreated sewage was pouring into the river by millions of gallons from known sources — so-called combined sewer overflows.

Some 50 of these discharge pipes dump untreated effluent into the river during thunderstorms and other, heavy precipitation events.

What the Watershed Council didn't expect to find, and is still searching for answers on, is why certain areas, such as the testing site near Schruender Park off Riverview Boulevard in Methuen, was showing high bacteria counts even during dry weather — an indication of raw sewage leaking undetected into the river.

"It's not uncommon for there to be illegal sewage discharges," said John Macone, policy and education specialist at the Watershed Council, which is based in Lawrence. "It's very hard to find — like finding a needle in a haystack."

The findings have been reported to the federal Environmental Protection Agency, "so hopefully they are looking into it," Macone said.

High amounts of bacteria in the river — which is the drinking water supply for many communities in the area, including Methuen and Andover — can be dangerous to swimmers, boaters and wildlife, according to the report.

Macone said the most common problem reported is gastrointestinal illness. A report done six years ago showed a direct link between emergency room visits and heavy discharges of stormwater into the river.

"When untreated sewage, stormwater, and industrial waste drains directly into the Merrimack from CSO events during heavy rainfall, (it) introduces pathogens and other harmful contaminants to surface water bodies where people swim, fish, and boat," the report said.

The pollution also "degrades habitat for species such as the endangered shortnose sturgeon," according to the report.

The discovery in Methuen was just one of many conclusions contained in the report, which detailed the organization's testing protocols and results, while also charting a path forward.

Watershed Council Executive Director Matthew Thorne said the Methuen "hot spot" near Schruender Park isn't the only place along the river that is showing spikes in bacteria.

"Where are these hot spots?" Thorne asked. "When we find them, we can fix them and we will be working with the EPA and Department of Environmental Protection on this. We're going to do a lot of Sherlock Holmes-ing this year. We have to get to the bottom of this."

The good news is that the testing located hot spots of high bacteria, giving investigators a good idea of the general area of what could be an illegal pipe dumping raw sewage into the river, or a break in an existing pipe.

"Now, at least we know where to look," Thorne said. "We know which haystack to look in."

The monitoring program, conducted throughout the winter, will pick up speed again in the summer, while other initiatives continue as well.

In particular, the Watershed Council is teaming up with Newburyport to conduct a pilot program that would inform residents when to expect high levels of bacteria in the water. Notification will be done through social media, email, website headlines and other means, Macone said.

That pilot program will be expanded by the end of next year to include communities up and down the river, he said.

Meanwhile, state legislation was passed last year requiring every sewage treatment plant along the Merrimack to notify the public when raw sewage is discharged into the river.

At the federal level, Congresswoman Lori Trahan is working on getting grant money or low-interest loans to help river communities in their efforts to improve the pollution problem by separating drainage and sewage pipes.

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