Though far from a wilderness experience, the upper Mystic River is a great place for a half day urban adventure if you are in the area. In all but the highest water (flood/spring) conditions, it is easy to put in upstream (just below the lower of the Mystic Lakes), paddle as far as you are inclined, and return upstream. I prefer to paddle the upper section of the Mystic River, as I typically paddle a tippy solo canoe, and am not interested in the lower section (see other review of the Mystic) because of wind and boat traffic.
I enjoy seeing an unusual side of Medford/Somerville- and especially going under numerous bridges. I always mean to count- it's close to a dozen- but then daydream and forget the number. I've seen large snapping turtles, numerous blue heron and night heron, and even otter. Occasionally there is motor boat travel, but most everyone has been respectful and slowed down. And sadly lots of trash. But I come back here again and again because it is a surprising slice of the city, with an easy travel time if you are north of Boston.
The easiest put in is either on the Lower Mystic Lake, or the upper river, as it turns into the river. Just north of Route 60 in Medford (or High Street) on the Mystic Valley Parkway. This in not far from from the Alewife/Mass Ave in Cambridge/Route 2 interchange. I typically just park on the street, and have never had a problem.
Mystic River Watershed Association at http://mysticriver.org/