We got in on the Charles, on the north bank, near the science museum. Boat traffic can be heavy at times, especially in the summer when the duck boats are out. From there you go under the new I93 bridge. Note the keyholes cut out in the central reservation to let light in - this is apparently to reduce the likelihood that fish will cross the shadow caused by the bridge.
Getting the attention of the lockmaster to close the gates was tricky - a strobe or horn could be useful. We dropped between 5 and 10 feet - this is obviously dependent on the tide in the bay. We timed our trip to coincide with the tide coming in. From there we traveled out around Charlestown, past the USS Constitution, and under Route 1 into the Mystic. At this point the river is very industrial (and tidal). There can be ocean-going freighters in this channel, so beware. There are also signs of past industry, with old cranes now being used as roosts.
Heading north you pass under the orange line T, and toward the Amelia Earhart lock. We had even more difficulty getting the lockmaster's attention - he commented that he had never seen non-power boats going through the lock. From there the river narrows until and winds even more, especially as you go through Medford. You could continue north to the Mystic Lakes and get out there, though there may be a portage at the mouth of the south lake.
A nice paddle combining downtown sights, locks, US history, industry, ocean tides, and a small winding river. Total distance was about 8 miles, time about 2 hours (depending on tide).