in the sea—in the waters of the sea:
- These fish are found in the seas along the North Atlantic coast of America.
on the sea—
1. on the surface of the sea:
- On the sea ice seldom forms smoothly. Early storms break it and pack it in confusion.
2. on the coast, close to the sea-side:
- The duke abandoned the city of Benevento and went off to another city, which was situated on the sea.
Note: Neither expression correlates in meaning with the phrase at sea—
1. (of a ship) far away from land:
- If he knows Morse code, he may listen to messages from ships at sea.
2. (also: all at sea) perplexed; confused:
- The job was new to me, and for a few days I was quite at sea.