When Mashpee Shellfish Constable Donovan McElligatt headed up the Mashpee River on August 27, to tend to some aids to navigation, he was struck by “the odor of almost raw sewage on the river.”

Rounding the corner toward the town’s oyster aquaculture site, Mr. McElligatt noticed “suspended solids floating down the river,” he told the Mashpee Shellfish Commission at their meeting at Town Hall on September 14.

“The water was not brown,” Mr. McElligatt said, hyperbolically. “I had never seen water that color before, outside of a glass of chocolate milk.”

The shellfish constable said he immediately took a water sample. The next morning, when he returned to check on the about 4.2 million oysters growing along the riverbank, he found that the shellfish were “all showing signs of severe stress.”

With the help of volunteers and Mashpee Department of Natural Resources staff working overtime to “emergency pull” the shellfish from the oxygen-starved conditions in the river, about 4 million oysters—almost $200,000 worth—were rescued and relocated to a sandbar downstream, Mr. McElligatt said.

For decades, scientists who study coastal embayments have warned that pollution from the thousands of septic systems that dot the region’s watersheds has led to a continuous decline in water quality in Cape Cod’s bays and estuaries.

After years of delay, Mashpee Town Meeting this past spring approved the first phase of a five-phase plan to replace septic systems throughout the town with sewer systems connected to wastewater treatment plants. Construction of the first phase, which focuses on the Mashpee River watershed, is expected to begin next spring.

Even so, earlier this summer, the University of Massachusetts Dartmouth scientist who studies Mashpee’s waterways, Dr. Brian L. Howes, reported to the Mashpee Board of Selectmen that for the first time in 20 years he had “nothing good to say.”

Both of the town’s bays now show impaired water quality throughout, algae blooms are increasing in frequency and size, and fish populations will begin to decline—if they are not already in decline—Mr. Howes said.

The nitrogen-laden effluent discharged by septic systems washes through Cape Cod’s sandy soils and concentrates in estuaries like the Mashpee River, one of the region’s most nitrogen-polluted estuaries.

There, the excess nitrogen acts like fertilizer, causing algae to grow out of control. Every summer, the Mashpee River is bedeviled by blooms of algae that have long since smothered native plant life like eelgrass, which once provided ample habitat for wild shellfish populations.

As the algae dies off, it can generate an unpleasant stench and the process of decay can absorb oxygen from the water column, creating dead zones where life cannot survive.

After consulting with experts, Mr. McElligatt said that is what he believed happened in late August in the Mashpee River.

“Due to the high heat that we had in August as well as a lot of freshwater rainfall, all of the benthic algae at the bottom started to die and rise to the surface—which was the suspended solids we saw,” Mr. McElligatt said. “As [the algae] started to die it started outgassing, releasing a lot of nitrogen which caused kind of a hyper-bloom in the river, which then caused the DO or the dissolved oxygen in the river to crash, pretty dramatically.”

In addition to the shellfish that had to be rescued, Mr. McElligatt observed “really, really low” levels of dissolved oxygen in the river and “started seeing dead blue crabs everywhere,” he said.

“We didn’t notice a fish kill per se, but talking with a couple experts they theorize there is no fish kill because there are no fish there to begin with; they had all kind of left the river,” Mr. McElligatt said.

Peter Thomas, the chairman of the Mashpee Shellfish Commission, was among the volunteers who helped rescue the oysters from the Mashpee River.

“It was like a war zone,” Mr. Thomas said. “We’re not going to have anything to save by the time the sewer plant treatment is running; that river is circling the drain.”

The volunteers and natural resources staff “busted their butts” to drag the oyster cages from the water and by boat to the sandbar near the basin of the river, Mr. Thomas said.

“God only knows what would have happened to all those oysters out there a few more days,” he said. “A great reaction on very, very short notice, and you saved the town a lot of money and a lot of shellfish.”

While the conditions in the Mashpee River have forced the natural resources department to reconsider its shellfish propagation strategy there, there is a silver lining, Mr. McElligatt said.

The oysters are thriving at the sandbar where they were relocated to, he said. Clearer water and less mud along the bottom makes the site easier to work at than the location along the edge of the Mashpee River, requiring fewer staff and hours for the same amount of shellfish propagation.

Mr. McElligatt said he hopes to turn the sandbar site into a nursery that can serve as “a giant pair of lungs for the bay,” where young oysters will be grown before being moved as adults to the areas in the Mashpee River.

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