I'm less than a mile away from the Charles River. It was terribly polluted in the 19th and 20th centuries by raw sewage and industrial waste, and unswimmable. Thankfully in the past few decades serious efforts were made to clean it up, and now it's safe to swim in most of the year, and hosts swimming events throughout the year. However it's still not a common recreational swimming spot, partially due to the stigma, and partially due to some water quality concerns that still remain. Sometimes bacteria levels can be at unhealthily high levels after heavy rain (though thanks to improved infrastructure this problem is nowhere near as bad as it used to be, and the current water quality can easily be checked online) and there is still some toxic crap left sitting at the floor of the river (not an issue as long as you don't touch the bottom). Regardless of water quality people enjoy it all the time through boating, and biking/walking along the banks. Every Sunday the road on one side is closed to cars for a stretch so pedestrians and cyclists can have it to themselves.

We have a bunch of ponds around the Boston area, but many of them are reservoirs used for drinking water, so you're not allowed to swim in them. However if you're willing to drive a little outside the city, there's plenty of fresh water to swim in including the famous Walden Pond.