It'll be fine. That's the way young BC develop in the wild. If they couldn't be submerged as seedlings, they'd die. I would however, keep the water level a bit lower--like the bottom third of the container. That will allow some air exchange. BC can survive submersion up until a certain water depth (don't worry, you can't exceed it in a container, unless you drop the pot to the bottom of a swimming pool). A little shallower water depth in the pot, however, can help things along...
Don't expect knees to develop. That is very rare with bonsai BC.