While that’s an impressive accomplishment, it’s unfortunately not the whole story. The EPA’s grade is only for E. coli counts in the lower Charles. Those nasty bacteria are mostly contained, but now the Charles faces a double threat — the combination of stormwater runoff and climate change.

The Environmental Protection Agency has graded the Charles River on its water quality each year since 1995 when it earned a D. In years hence, major improvements to sewer systems in Boston, Cambridge and beyond brought the grade up to where it stands today. The river is now safe for boating 95 percent of the time and safe for swimming about 70 percent.

“Stormwater runoff is the number one source of pollution in the Charles River,” said Bob Zimmerman, executive director of the Charles River Watershed Association, speaking of this year’s EPA grade at the Museum of Science on July 27. Rainwater coming off roofs, streets and parking lots runs into storm drains and eventually to the Charles. On its way to the river, the water picks up phosphorus and nitrates that originate from detergents, fertilizers, soil and motor oil.

These pollutants in the stormwater raise havoc with the ecology of the river. Although tiny amounts of phosphorus are naturally present in freshwater, in the higher concentrations stemming from stormwater runoff, it acts as a nutrient that turbocharges the growth of algae and some types of bacteria.

Midsummer is when noxious algae outbreaks tend to appear. Last August, the Charles experienced a bloom of cyanobacteria, also known as blue-green algae, causing some parts of the river to turn pea soup green and give off a fetid stink. Besides being just plain gross, cyanobacteria produce toxins that are dangerous for people and animals. The Department of Public Health had to warn people to avoid contact with the water or risk health problems.

Because of its instrumental role in algae blooms on the Charles, stormwater runoff is already by itself hugely detrimental to the health of the river. Climate change multiplies the threat. Runoff and climate change are perversely linked such that the effects of one exacerbate those of the other.

Higher water temperatures increase the likelihood and severity of algae blooms. Until just recently, a power station in Cambridge was releasing 70 million gallons of heated water into the Charles each day. The plant now avoids the discharge by using the excess energy to generate steam heat for buildings in Boston. The hope is that the reduction in thermal pollution will lower the river’s temperature and limit cyanobacteria.

But a warming climate may dash that hope. “As we get warmer and warmer, the threat of cyanobacteria blooms will increase," according to Zimmerman. This year is on track to be the warmest on record. Over the coming decades, a rising water temperature due to climate change is sure to worsen runoff-fueled algae blooms.

And heat is not the only way climate change intensifies the harm from stormwater. Studies predict that global warming will lead to periods of drought punctuated by short, violent storms. In that kind of weather pattern, rainwater that under more moderate conditions would percolate into the ground, instead washes into storm drains. The net result is more phosphorus in the river to feed the algae.