Boston harbor is a series of bays and river inlets including Quincy Bay, Hingham Bay, and the inner and outer harbors. The is watershed is fed mainly by the Mystic River, Neponset River, and (at one time, since dammed) the Charles River. It is a protected harbor, but it's nowhere near Cape Cod (take a look at a map -- the cape is farther south). Rather, the inner harbor is protected by a series of oblong islands, and the peninsula of Hull forms Quincy bay.

Most of the harbor islands are now a series of state and national parks. One of them, George's Island, has been the site of a fortress in every major war for the past three centuries, including the Revolutionary War, the Civil War, and World War II. It's a great day trip out from the city. Another, Deer Island, is the home of Boston's new waste treatment plant, and the primary reason you can now swim and fish in the harbor. Not sure if you can actually eat the fish you catch, but the fact that there are fish now is a big step.

Sources
http://k12s.phast.umass.edu/~masag/watershed/bostmap.htm
http://people.ne.mediaone.net/pennypenguin/Maps/BostonHarborMap.html
http://www.nps.gov/boha/
http://www.bostonislands.org/park/

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