Segments of the Neponset River, once considered a dumping ground for industrial companies looking to offload raw sewage and pollutants, have received water quality grades of B and C+ from three Boston watershed groups.

The groups announced the letters earlier this month in concert with the US Environmental Protection Agency. The announcement came as the groups marked the 50th anniversary of the Clean Water Act.

The water quality report cards also graded the Charles and Mystic rivers.

The Dorchester and Mattapan segments of the Neponset fell in the “B” category. The “C” category included the parts of the Neponset that run close to Milton, Westwood, and south of Norwood and Canton.

“The biggest challenge to the Neponset is polluted stormwater runoff from streets, parking lots, and yards,” said the report from Neponset River Watershed Association, the Mystic River Watershed Association and the Charles River Watershed Association. “When it rains, pollutants on our roadways and parking lots — oil, gas, bacteria, pharmaceuticals, and more — are washed directly into our waterways.”

Ian Cooke, head of the Neponset watershed group, said that while the Neponset has improved over the last 40 years, the polluted stormwater runoff is still a “huge problem.”

The Lower Neponset River was recently designated by the EPA as a “Superfund” site, which will help provide money to clean up contaminated river bottom sediments.

“As a Dorchester resident, I dream of the day when residents along the Neponset River Watershed can swing these waters with joy,” said Rev. Mariama White-Hammond, Mayor Michelle Wu’s environmental chief.

“I am grateful for Boston’s partnership with the U.S. EPA and our three watershed organizations, and I look forward to our continued collaboration.”