My first drowning fort was in 28.40d. My embark area had a brook that ran on top of a rock mesa, and the mesa also had a bottomless pit.
I originally build straight down. Built a starting "entrance" chamber, fairly down from the surface (took it down to the first layer of the mesa that had soil on the side near my starting spot). The starting chamber was just somewhere to keep my idle dwarves underground, and my starting stockpile area. Then I got to work digging out my fortress, setting up farms, workshops, bigger stockpiles and moving out of the entrance chamber.
Originally, I was thinking about filling the entrance with weapon and cage traps and setting up fortifications that could shoot across the chamber, so I could just have my marksdwarves pincushion attackers. Then I noticed that the bottomless chasm was a short distance away from my entrance chamber, and the brook wasn't that far away either, just several z-levels up. I got to thinking about setting the chamber up so I can just flush attackers away into the chasm ("THE COMMODE OF DOOM!"), but I ended up just digging out a gravity fed plumbing system so I could shut the entrance off from the rest of my fort, and then drown anyone in the entrance chamber. A few floodgates, a few levers to control them, and I had myself a nifty drowning system which could be drained into the chasm at will.
I even chained up some animals in the chamber, setting them just a bit off from the stairs so they wouldn't get immediately shot up by the attackers, and I put in floodgates to keep them from drowning so I wouldn't have to keep replacing them whenever I drowned attackers.
The first six waves of goblin siegers died in the chamber, as did over a dozen "ambushing" goblin forces, with all members lost in the chamber. Finally, one goblin got out of the drowning death trap, by holding his breath FOR A MONTH, getting to the up/down entrance stairs, and swimming/climbing up to the surface. After that, none of my goblin attackers ever came down into the flooding chamber, even if I activated a sacrificial dwarf and stationed him or her at the bottom of the stairs. Seriously. They would only come down by CHASING a sacrificial dwarf from the surface. One level down on the stairs, they'd still ignore. Funniest thing. I decided it was due to the horror stories of that original surviver, spreading through the goblins.
I also constructed massive cisterns that I could use to drown attackers, just in case I ever got a deep winter attack. The brook froze up for part of the winter. Right after I finished my cisterns, I got a winter siege. The timing was quite fortunate for me that it took that long, rather than before, when the brook would have been unavailable.