I've created a room with knee-deep water where I have also put a slaughterfish. Will navmeshing the floor be sufficient for this slaugherfish to be able to move around and also use its AI?
Or is there some special procedure for water-based actors?

If the water is deep enough to swim in you mark the triangles as water navmesh with 'O'. However if it's only knee deep I'm not sure if you should do that or not. Try it with and without marking it as water and see what happens.

If you could report back that would be awesome, as we were trying to figure out how deep water needs to be to be marked as 'water' navmesh.

I have water in my u/g cave and slaughterfish. In order for them to work properly, the water had to be about chest deep, and I toggled the navmesh I created aas "O" for water navmesh.

The slaughterfish worked fine; however, I have had one instance where one jumped up on land to attack a follower before she one-shotted it with a lightning bolt.
I laughed; it was awesome!