I've not seen this done with water channels before, im guessing you want to train swimming on your army as they dodge traps? Very nice idea.
Heres why they drown:
When a dwarf submerges he gets stunned, this means its a little while before he can climb the ramp out. A creature with 0 swimming whatsoever has a great deal of difficulty moving while submerged, so my guess is your recruits just dont manage in the window after they unstun and before they drown. This should vanish very quickly, even a novice swimmer should probably make it out all the time if they are just falling onto a 7/7 ramp back up. (you do have a ramp right? exiting without one requires a more serious degree of swimming skill). Experiment in adventure mode as a dwarf with varying levels of swimmer to see what you are happy with them dealing with.
Unfortunatly training swimming without risk of drowning is very hard if the creature is starting from 0. If you must have swimming military then heres some ways to tweak the game (mod):
Give your dwarves [NO_STUN] - no regen needed, once they hit novice you could take this off again, it also gives dwarves an extra edge in combat.
Give all dwarves Novice swimmer to start with - needs world regen
Look into a custom workshop to train swimming. I can highly recommend the swimming pool from Deon's Genesis mod, manager profile it to only be used by military and set swim to repeat, when off duty they will do a few laps once in a while and skill up to the point where they can survive your danger room - regen world required (i think, new reactions n all)