By default, attack rolls made while the attacker is underwater have disadvantage.
For creatures that can't breathe underwater, use a standard countdown (3) to track how long they can hold their breath. Advance the countdown whenever the PC takes an action. In addition if they fail a roll or roll with Fear while underwater, you can spend your GM move to advance it an additional time—or twice, if they rolled a failure with Fear.
Once the countdown ends, the underwater PC must mark a Stress whenever they take an action.