It's possible for the player to use a flower to lead bees into water, drowning them.

Steps to reproduce:
1) Obtain a flower

2) Get a bee to follow the player

3) Wait until bee lowers itself to ground level

4) Walk into water, while holding flower

5) Let bee follow player into water

The bee will follow the player holding the flower into a body of water. As the bee lowers itself to ground level, it will take damage from being in the water and drown. It does not fly above the water to keep from taking damage.