You asked about the meaning of the following:
A. He is on the sea.
B. He is in the sea.
C. He is at the sea.
D. He is underwater.
In A perhaps he is in a boat on the water (he is not on land).
In B perhaps he is swimming in the sea, not in a boat.
*C is not quite idiomatic; we usually say either
C-1 He is AT SEA. (=perhaps he is a sailor and his boat is now at sea, not in port) OR
C-2 He is AT THE SEASIDE. (=at the beach)
In D, he is under the surface of the water, perhaps swimming or searching for something in the water.