There are a total of 40 crates underwater that you have to destroy. You do this by swimming up to them and lightly touching them then swimming away before they explode. Just be thorough and make sure you get all of the crates. When the last one blows up, you'll get the skill point.
This is also 1 of the 30 skill points needed for
Here's a video, thanks to StillTheCinema, that could help if you're having trouble finding the crates. This trophy starts at 4:27