iirc, atom smashers also smash water. You can make a large chamber with a bridge covering it, dig out the wall in-between and destroy water as it flows in. This might slow down the flow enough so you can close it off somewhere else.
It's possible but there's no point because the map edge is better. If you want do this though, then the first thing to know is that you need to use "bridge walls", only the tiles which actually turn into a raised bridge actually smash water. The bridge part going up and down just sloshes the water around. Important to know that. The other than is that doors open/shut instantly, while floodgates and bridges have a significant delay. A door linked up to a dwarf pulling a level will smash water at a blistering rate.
Atomsmashing water is really more applicable for things like selectively lowering the water level of a pool, or for use in fluid logic or water repeaters. For actually disposing of masses of water, the map edge or a cavern is a much better way to go, partly just because it's a pain trying to figure out how big the atomsmasher needs to be to destroy the water fast enough, while the map edge will accept water at an infinite rate.