Ebony,
Lots of season 2 was filmed in south baltimore/locus point. The bar that all the dock workers went to was at the southeast corner of E Clement St and Jackson street. It was called the Clement Street Cafe. My parents used to live on harvey street right behind it and I would come home sometimes and see the film crew out front of the bar. If you stand in the middle of the intersection you’ll see the Domino’s sugar sign at the end of the street. They had several shots in the show with that angle. Around 2003 they converted the bar into a couple condo units.

old clement street cafe- http://maps.google.com/maps?q=636+harvey+st+21230&hl=en&ll=39.274042,-76.60518&spn=0.001719,0.003363&sll=37.0625,-95.677068&sspn=56.856075,110.214844&vpsrc=6&hnear=636+Harvey+St,+Baltimore,+Maryland+21230&t=m&z=19&layer=c&cbll=39.274034,-76.605342&panoid=IcoUwHRsyEhWq8DUZqUraw&cbp=12,145.46,,0,0.5

The grain terminal they make reference to several times in the show was kind of based on reality. There used to be an old grain pier to the old ADM grain facility in Locus Point. The pier collapsed into the water around 1999 and ADM didn’t want to pay to get it fixed. The facility closed shortly afterward. The last episode has one of the young polish guy (cousin?) looking out at the ADM grain facility (big ugly concrete silos). That was shot off of Fort Avenue right as you’re about to get on the bridge over the rail lines to Ft Mchenry.

The below street shot is present day close to where it was shot. The grain facility was converted into high end apartments and the fence where the scene was shot are now big row houses (eluded to in the last episode of season 2).
http://maps.google.com/maps?q=636+harvey+st+21230&hl=en&ll=39.267007,-76.587989&spn=0.006878,0.013454&sll=37.0625,-95.677068&sspn=56.856075,110.214844&vpsrc=6&hnear=636+Harvey+St,+Baltimore,+Maryland+21230&t=m&z=17&layer=c&cbll=39.266935,-76.587845&panoid=50jF_oEWhI8GrwbfkDjFPw&cbp=12,342.17,,0,-0.07

The place where Sobotka meets the greeks for the last time was under the Key bridge (I-695) in baltimore county. The place where his body washes ashore is the Port Covington dock facility ( I think) in Locus Point. The rest of the dock scenes were probably done at the Dundalk facilities.

Some other South baltimore moments were when Stringer Bell and Bodie meet in season 3 to talk face to face about hamsterdam. That was the museum of Industry off of Key highway.

One episode, I forget which episode, when mcnulty gets drunk hears a car alarm go off, stumbles out of the car and falls down a hill, That’s actually Federal Hill. They briefly show the car and people running away on Covington Street right by the American Visionary Art museum. The building in the background was abandond at the time but now is a part of the museum.