Jump Bug (late 1981) is the earliest. It has an entirely underwater level, and the car moves more slowly in it. It was also one of the earliest platformers, beaten only by Donkey Kong (mid 1981) and a couple others.

Super Mario Bros. (1985) introduced a significantly different mechanic for its water levels from the rest of the game, specifically swimming, and it was about a bajillion times more popular than Jump Bug. But it wasn't the first.

Sub Hunt, Frogger, White Water

I'm worried that you may be a time-traveler with a gruge.

If you mean "water level" as in where for an isolated level you're swimming, but not the entire game, super Mario Bros might be it