We now have a shower head that has stones/pebbles or pumice stones that the water can flow over from the tap. The stones are meant to do something to the water, is this water okay to purify myself with?

All perfect praise be to Allaah, The Lord of the Worlds. I testify that there is none worthy of worship except Allaah and that Muhammad is His slave and Messenger.

The fact that the water runs over the stones which you mentioned usually does not change it [water]; even if we presume that this changes the water, it does not change it to a point that takes away its characteristic of being a purifier. Rather, it is a slight change that does not affect it.

An-Nawawi said:

“If the change is significant, then it negates its role of being a purifier, but if the change is slight, like if some saffron falls into it and it becomes a little bit yellow, or if soap or flour falls into it and it becomes a little bit white, in a way that it is not attributed to it in principle [such as saying flour water, or soap water], then there are two views about this: the most correct opinion is that it purifies as its name remained the same (i.e. absolute water); this is the view considered by the Khurasaani scholars (in the Shaafi'i School) to be correct, and this is the chosen opinion.”

Also, Kash-shaaf Al-Qinaa‘ 'An Matn Al-Iqnaa’ reads, “If a slight amount of a pure substance mixes with it and slightly changes one of its characteristics, then it does not negate its fact of being a purifier.”

Accordingly, there is no harm caused by purifying yourself [performing ghusl] with the water that passes through the stones mentioned before it reaches your body.

Allaah knows best.