The Promenade along the Inner Harbor is the signature running option in Baltimore. Various route options incorporate the more touristed sections of the Inner Harbor, historic Fort McHenry, and the more neighborhoody sections on the northern side of the harbor, and the more industrial sections in on off Clinton St. This area features a brick path (be careful of the occasional brick sticking out), some sections of wooden pier, cobblestones in Fells Point, and a handful of pedestrian bridges.
The signature run is from Inner Harbor to Fort McHenry and around the fort, 3.2 miles one-way. This includes Under Armour HQ, owner of MapMyRun, at the top of the harbor. On the northern side, two good options: Starting at Harbor East, Aliciana St. down to the Boston Street Running store and loop back for a 4 mile run. Boston Street is a great street to run on, as it is filled with runners as early as 5 am in any kind of weather. You can extend the run by turning south on Clinton St., which is also on the water but has a more industrial feel. Another nice detour is the Federal Hill neighborhood. Some nicer older homes and also Federal Hill Park. Great view from the top.