I remember hearing that the Charles river was safe enough to swim in years ago now that it has been "cleaned up". Then I realize I swam in the river as a kid long before it was cleaned lol. I may be wrong but I think I remember reading somewhere that back before it was cleaned it was advised that it you were boating in the Charles and fell in you should go get a tetanus shot.
I swam in the Charles when I was a kid too a few times, so far no mutations
. When the herring would run we used to wade through the water to the fish ladder and hold a net to catch the herring which we used for bait. During that time of year some pretty large stripers would follow the herring into the Charles and makes for some good fishing, would not recommend eating what you catch though.