Many of them do that. Just make sure the water is not too deep, warm and in a safe place where it doesn't cool too quickly. In time they get used to it, and its good for them, even though some of them act panicky at first.
My sulcata Daisy was like that at first. I don't think she had seen much water before I got her at three months. It took several months of daily soaking her to get her to just calm down a little. Now, at three years old, she's totally fine with the water and growing up nice and healthy.
None of my hatchlings ever "freak out" like that since they are wet and in water from day one.
If you're worried about him not drinking enough, put a source of water in his enclosure and see if he will approach the water on his own.
Is this tortoise new to you? I've gotten tortoises that were either stressed or were not used to being soaked and would not stay still in the water at all long enough to drink anything. After a few days they either calmed down or realized what the water was for and I don't have this issue anymore.
I could see where a Glass bowl would cause stress metal also... they vibrate and metal echos. mine dont quit moving when theyre in their soak... but they dont freak anymore either... and today it looked like they were trying to swim!