The answer is Yes and No. There was a time when Boston Harbor was one of the filthiest, most polluted harbors in the nation. Swimming and fishing were all but unheard of.
The cause of the famous sludginess was that the sewage being pumped into the harbor was only partially treated, resulting in grades of "D" or lower for water quality over the years.
A series of lawsuits in the early 1980s resulted in the city cleaning up its act - and its water! The courts ruled that sewage must be properly treated, and after several years of stalling and expensive red tape, Boston built a brand new, state-of-the-art treatment plant on Deer Island which now serves 2.3 million people.
Each of the 12 giant, egg-shaped containers holds 3 million gallons of solids filtered from Boston's 360 million gallons of wastewater per day - Yuck!
94% of the total solids are removed from the wastewater, which then gets disinfected and dechlorinated before finally being sent out into Massachusetts Bay for final disposal.
As a result of the goings-on at Deer Island, Boston Harbor's ecosystem has improved greatly. According to the plant’s Director, David Duest:
"We haven't had any permit violations for over eight years now and we're actually seeing a recovery of the harbor so that things like Eel grass are actually naturally reestablishing themselves back into Boston Harbor. Eel grass is a very sensitive natural species of sea grass that only grows when the water is very, very clean."
Well, there you have it! Boston's water is dirty no more - we still love the song, though!
H/T to Living on Earth