with which to make

Its correct, just kind of awkward. Lots of emphasis on the water used to make the soup for seemingly no reason.

Not a native speaker here, but for me it doesn’t sound right. With which you make the soup - sounds a bit better. And even then “which” is usually used to point to one thing out of a row of similar things, so it doesn’t work well with “water”.

Doesn't make sense? Sure, but it sounds really unnatural. Most people would just say "the device filters the water *for* the soup." Or "the soup is made with filtered water."

the device filters the water that you make the soup with the device filters water that you use make the soup with the device filters water for making soup with the device filters water for use in soups Many ways to say this kind of thing, but yours is awkward.

It's OK, but I'd probably just say "The device filters water for making soup."