There is nothing wrong with trotting through water. If your horse lands in canter, great, but if you find yourself in trot when going through water, just push/hold the trot together and keep it that way all the way through.
Trying to pick up canter in water is not easy, and you might well get a sprawly unbalanced canter that the horse doesn’t feel it can jump from. I saw a friend have a stop at a fence in water at a CCI*, ruining their chances of a very good placing, when exactly that happened.
<< this is the offending fence, which jumped absolutely fine from trot, as you can see.
A horse can easily manage a big jump from a good trot. In my case (Savernake Advanced in 1999, to prove I’m not making this up!) it was two big steps up to a biggish flowerbed, without a problem!