A woman kayaks in the Charles River. (Jesse Costa/WBUR) The Charles River’s annual water quality report card from the Environmental Protection Agency looks pretty good: four A’s, one B and — one D-. But wait, mom! There’s an explanation! For the first time, the EPA graded each section of the Charles separately, and also included two tributaries: the Stop River and the Muddy River. It was the Muddy River, running through Boston and Brookline, that got the D- for high levels of toxic algae and E. coli. But it wasn’t totally the river’s fault, says Lisa Kumpf, an aquatic scientist with the Charles River Watershed Association.