The EPA reports it's given the Charles River an A- for cleanliness in 2013:
Reflecting nearly twenty years of focused efforts by EPA, state and local officials, private environmental advocacy groups and concerned citizens, this is the first time the Charles River earned a grade higher than “B+”. As with past years, the grade is based on bacterial sampling conducted by the Charles River Watershed Association during the previous year.
The latest grade reflects continued improvement in the number of days the river is safe for boating and swimming. For the 2013 calendar year, the river was safe for boating 96 percent of the time and safe for swimming 70 percent of the time, representing the highest safe swimming percentage in the past 19 years since the Charles grade was first issued. This is a notable improvement over the past several years and a dramatic boost from 1995 when the River met boating standards only 39 percent of the time and was safe for swimming just 19 percent of the time.