Charles River at its cleanest in at least two decades

The Environmental Protection Agency says the waterway has never been cleaner since testing began in 1995. Pat Greenhouse/Globe Staff

The Environmental Protection Agency on Wednesday released the results of an annual test of the Charles River, which revealed the water is the cleanest since testing began in 1995.

The test, conducted on samples collected by the Charles River Watershed Association, looks at the quality of the river water and determines what percentage of the time it is safe to swim and boat. For 2013, the river received an A-, its first grade above a B+.

The EPA gave boating a score of 96 percent and swimming 70 percent, meaning it is safe to boat 96 percent of the time and safe to swim 70 percent of the time. While those numbers are not perfect, they reflect a substantial improvement from the 1995 scores — 39 percent and 19 percent.

That is “a pretty dramatic change over less than 20 years,” said Emily Zimmerman, an EPA spokeswoman. Zimmerman said the improved water quality is a direct result of scientific studies. “There have been all kinds of water quality monitoring and studies done about what’s polluting the river,” she said.

Since the Clean Water Act of 1972 prevented companies from dumping waste into the river, most of the pollution has come from sewage lines connected to storm drain systems, said Bill Walsh-Rogalski, an attorney for the EPA.

Still, the pollution level is improving with projects directed at eliminating pathways for sewage into the river, Zimmerman and Walsh-Rogalski said.

In 2013, the Boston Water and Sewer Commission eliminated illegal drainage into its storm drain system, removing more than 2.7 million gallons of sewage from the Charles River drainage basin, the EPA said.