Mark C is dead on about Western Run and Jones Falls. Both are very difficult fishing because of brush. Great streams for destroying your waders. That said, both are excellent brown trout habitat. I've probably caught more wild browns out of those two streams than any others I have fished -- but I did live within bicycle range of Western Run and its tribs when I was a kid. My second biggest brown trout came out of a Western Run trib when I was 16 years old. It's 45 years later and I still fish both creeks at least once a season because they are among a few spots in Maryland where you always have a non-zero chance at catching a bruiser. And I'm not spot burning on this. If you show up thinking you're going to sling a nightcrawler and catch a stringer full of fish, you are in for a rude awakening.
Jones, Western, and Big Gunpowder and most of their tribs are on strong aquifers that qualify as limestoners, but the springs are relatively small. Strictly speaking, the creeks also have a lot of freestone water in them. In the north end of Baltimore County, Western and Big Gunpowder springs are on the Cockeysville Marble Aquifer, and Big Gunpowder itself has the advantage of being a tailwater out of Prettyboy Reservoir.
Wild Trouter's link goes to a thread that includes a link to a geological survey of all of Maryland's springs, which is a good resource. The thread also references Glade Creek (sometimes called Fountain Rock Creek) near Walkersville. There used to be a private hatchery and pay-to-to-fish spot in what is now Fountain Rock Park. When I was a kid, there were hatchery escape rainbows, but the stream was in terrible shape then, and probably worse now. It flows maybe a mile from the park to the Monocacy River, all on farmland. Mainly it's plowed to the bank, so it's wide, shallow, no cover and silted over runs. I fished it about two years ago and didn't even see a fish (not even a chub). The creek has tremendous potential because of the size and resilience of the spring, but a lot of bank restoration is needed (similar to what was done over on Beaver Creek years back).
Coming out of the same limestone formation is Carroll Creek. It's in very rough shape, particularly in the park in the city of Frederick, probably beyond saving. The upper sections (to the west of U.S. 15) used to hold trout, but I haven't bothered with them since the mid 1980s. Very tough fishing over a remnant population at best.
Antietam Creek is heavily limestone influenced, from its headwaters down to where Beaver Creek flows in. In Maryland, it is managed as a rudimentary put-and-grow creek. It gets a lot of hatchery leftovers (fingerling browns and rainbows) from the Beaver Creek station. There are some excellent places for fly fishing, but they tend to be short and and are scattered throughout the basin. There's a lot of posted water, and some of its tributaries are small limestoners. It holds a respectable number of decent fish and is also a Maryland spot where you could hit a big trout. But, again, not really spot burning here because it's difficult fishing. The bait guys do hit Antietam, and they take a few fish, but a lot of times they're following the hatchery truck and keeping literal fingerlings. There are some wild fish, but the creek is silt-heavy, so the supplemental (and unpredictable) fingerling stockings are what make the stream a decent near-limestone option.
My understanding is Conococheague Creek is another limestone influenced big stream, but that's all I know about it aside from it's where Falling Springs Creek in Pa. ends up.
Going over to the eastern side, Conowingo Creek in Cecil County is limestone influenced and I've caught wild browns there, but it's in a steep ravine and the fishing is moderate at best. Beautiful scenery, though.