Major rivers in the greater Boston area got their annual water quality report cards Friday. The good news is the Charles, Mystic, and Neponset rivers all boast some As and Bs.

But there were troubling spots on the 2021 Three Rivers Report Card, like the Mystic Watershed’s tributary, Alewife Brook, with the lowest grade for a major stretch of any of the three river systems — a D.

Andy Hrycyna, the watershed scientist for the Mystic River Watershed Association, said the spotty grades on some parts of the report cards for the three rivers tend to be on small tributaries that are disproportionately polluted.

"In particular, sewage pollution,” Hrycyna said, “believe it or not, in the 21st century in our urban areas.”

Hrycyna said Alewife Brook is an example of that, where there’s something called "combined-sewer overflow" going on at times.

These are situations where very old urban infrastructure directs both rainwater from the stream and sewage from our houses to the same pipe that's going to the Deer Island Wastewater Treatment Plant,” Hrycyna said. “But in really heavy rainstorms, that pipe can get overloaded, and, instead of backing up into our houses or onto the streets, it's literally designed to overflow into the nearest waterbody, which includes Alewife Brook, and includes parts of the Charles, and includes the Mystic River as well.”

The grades on the water quality report cards look at levels of the harmful bacteria E. Coli in all three river systems, as well as dangerous cyanobacteria blooms and combined-sewer overflow discharges in the Charles River Watershed. The report card is issued annually by three area watershed associations and the findings are reported to the federal Environmental Protection Agency.

Lisa Kumpf, the river science program manager at the Charles River Watershed Association, said that watershed is so much bigger than the Mystic, that even “sixty-three Olympic sized pools worth of sewage and stormwater that ran directly into the river” in 2021 only resulted in the Lower Basin of the Charles slipping from a B to a B-.

“Our lowest grade is actually in the Muddy River, which is a tributary in Boston and Brookline,” said Kumpf.

The Muddy River got a C-.

“And the story there is really due to the amount of stormwater runoff with impervious surfaces in that highly, highly urbanized area that runs into the river,” Kumpf said.

The impervious surfaces that affected that grade include parking lots, sidewalks, roads and large buildings, all which shed stormwater with collected pollutants from fertilizer, and even dog droppings, into rivers.

The Charles River Watershed Association and the Conservation Law Foundation are pushing the EPA to do more about polluted stormwater runoff in the Boston area’s three major rivers.

On Thursday, the two organizations sent a letter announcing their intent to sue the agency, saying it had ignored calls to protect the Charles, Mystic, and Neponset Rivers from runoff, mainly from industrial and commercial properties, and was violating the Clean Water Act.

The letter says CRWA and CLF would welcome discussion with the EPA on taking steps to solve the problem.

Another factor that has watershed scientists concerned is the current drought.State officials say 90% of Massachusetts is experiencing drought as of this week, with most of the state in “significant” drought.

“This is the third year of significant drought in recent years,” Kumpf said. “That definitely affects the water quality.”

“If we have lower stream flows, we have more concentrated pollutants, we have hotter water,” Kumpf explained, “which decreases the amount of dissolved oxygen that can stay within the water, which fish and other creatures use in parts of our watershed.”

Kumpf said that in 2020 some areas just downstream of local dams ran dry.

“And that is obviously a huge issue for fish passage,” Kumpf said. “They cannot move between parts of the river that don't have any water in them.”

Produced with assistance from the Public Media Journalists Association Editor Corps funded by the Corporation for Public Broadcasting, a private corporation funded by the American people.