It would seem that Scorpius used the Time-Turner while underwater
This isn't explicitly mentioned by the stage directions in the script, but they do describe a "bang and a flash" after Scorpius jumps into the lake (emphasis mine):
SCORPIUS thinks and then runs after the doe, and around him the world gets scarier. A bloodcurdling scream goes up at one side. He sees the lake and throws himself inside.
[...]
There is a bang and a flash. And then silence. And then there’s more silence.
The Cursed Child Part 2: Act III Scene 9
This is consistent with other uses of the Time-Turner; for example (emphasis mine):
[Hermione] takes the Time-Turner. It begins to vibrate, and then explodes into a storm of movement.
And there is a giant whoosh of light. A smash of noise.
And time stops. And then it turns over, thinks a bit, and begins spooling backwards, slow at first...
There is a bang and a flash and our gang disappear.
The Cursed Child Part 2: Act III Scene 7
It's also worth noting that it was always the plan to do this (emphasis mine):
Hermione: The first task of the tournament took place at the edge of the Forbidden Forest. We turn time here, get to the tournament, block the spell, and then return safely. With precision — it can be done and it won't require us to show our faces outside in our time at all. Then we'll turn time again, make our way to the lake, and reverse the second task.
The Cursed Child Part 2: Act III Scene 7
Ron: We need to use the Time-Turner again — get out of here —
[...]
Hermione: Reversing the next task will change everything.
The Cursed Child Part 2: Act III Scene 9
And the reason for Ron and Hermione's sacrifice is explicitly to give Scorpius more time:
Hermione: Let’s keep them here and give the boy the best chance we can.
The Cursed Child Part 2: Act III Scene 9