I’ve recently noticed water in my colony, and I found that this water basin was leaking slowly. [Edit: The white tiles were built after the fact to stop the leakage. Before that the water was just contained by the natural tiles you see.]
I don’t think the game explains this at all, so I’m asking here: Which materials allow water to pass through them, and which don’t?
No solid tiles allow fluids to pass through, with the exception of constructed tiles that are explicitly stated to be permeable.
See the white damage lines across the bottom tiles of that pool of water? Depending on the water pressure (ie amount of water on top of a tile) they will start to take damage based on their hardness (I think that's the stat, it's been a while), and eventually. More tiles makes it more resistant, up to 7(?) deep to never break.
I suspect the water leakage is from tiles about to break, but again it's been a while so I'm not sure. It's also possible you're getting a mess from somewhere else.