Corrected entry: The spaceship was sealed. Since they did not know the pressure of the air within the spacecraft, it can not be assumed it's the same as the ambient pressure, to which they were adjusted. Any change would have effected their bodies. Just as they had to adapt to the base station pressure when they first arrived.
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Correction: If you look closely, there is a small LCD display next to the airlock they enter through that displays "Adjusting Atmosphere". The ship automatically adjusted its own atmosphere to match what they were breathing underwater.
Grumpy Scot