Baltimore is a nice place to visit,but beyond the aquarium there isn't really a place for younger children. So try Port Discovery,the kid powered museum.My daughter and nephew love it,nothing like the kids actully ENJOYING something educational. Its not far from the Inner Harbor but a bit of a walk for little legs.They used to have a hot air balloon that you could take a ride in straight up but it malfunctioned once in windy stormy weather,never heard if they reopened it.
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