Filling up through a grate could work, so long as building destroyer doesn't have path to the grate. (Absolutely guaranteed if you have the water go through 2 sequential grates.)
I theorize that perhaps a statue flanked by fortifications might work as well, but have not tested this.
However, note that Brook's cyan surface acts as floor and spawns only vermin fish inside it - while I wouldn't claim the impossibility of an aquatic titan spawning in eight in 768 chance, I've yet to see any actual creatures inside one. (So yes, you can build walls over them.)
If you're on a map where cave-ins don't transform, you could also cave in the brook surface to desired point instead of using a grate.
And yeah, the two-stage filling with bridges (either raising to block sideways flow or retracting to block up or down flow) could work as well if for some reason you can't use grates.
There are some advantages to using floodgates over raising bridges, though:
1. A floodgate will not kill/destroy whatever less than enormous creature is caught in it.
2. A floodgate that failed to close at desired time due obstruction will automatically close once obstruction is removed. (Though note that if the signal is sent too soon after last toggle, the floodgate will ignore it.)
3. Every time a bridge toggles, it causes the map to stutter, even if it has literally 0 effect on the pathing of anything.
4. Raising bridge will let water through when "closed", floodgate when opened.
5. A floodgate can be destroyed by building destroyer - thus releasing water or magma to trap or drown or burn them.
But yeah, there are in-depth wiki articles on well & cistern design as well as bridges, floodgates, brooks. Though they don't contain quite all of the above :p