I also have several virtual machines which take up about 100 GiB.

This would be the first thing I'd look into getting rid of.

Could these just be containers instead? What are they storing?

nix store (15 GiB)

How large is your (I assume home-manager) closure? If this is 2-3 generations worth, that sounds about right.

system libraries (/usr is 22.5 GiB).

That's extremely large. Like, 2x of what you'd expect a typical system to have.

You should have a look at what's using all that space using your system package manager.

EDIT: ncdu says I've stored 129.1 TiB lol

If you're on btrfs and have a non-trivial subvolume setup, you can't just let ncdu loose on the root subvolume. You need to take a more principled approach.

For assessing your actual working size, you need to ignore snapshots for instance as those are mostly the same extents as your "working set".

You need to keep in mind that snapshots do themselves take up space too though, depending on how much you've deleted or written since taking the snapshot.

btdu is a great tool to analyse space usage of a non-trivial btrfs setup in a probabilistic fashion. It's not available in many distros but you have Nix and we have it of course ;)

Snapshots are the #1 most likely cause for your space usage woes. Any space usage that you cannot explain using your working set is probably caused by them.

Also: Are you using transparent compression? IME it can reduce space usage of data that is similar to typical Nix store contents by about half.