"You fill the glass with water."
Translation:Napełniasz szklankę wodą.
It's not assumed, it's simply not there.
Here the word "woda" is used in instrumental case, which is often used to tell what tool was used to perform an action. English would require an additional "with" to express it.
If you said "Napełniasz szklankę z wodą" it would mean that somebody and a water (through some arcane magic being able to perform voluntary actions) are filling the glass together.