John 2:7

To "fill" something is to endow it with a spiritual quality. The waterpots here represent the facts and ideas that contained the external truth of the Jewish church; the "water" represents that truth. The picture here, then, is of all the knowledge and truth of the Jewish church, everything they had to help them live good lives. It was external – about proper actions, not about proper thoughts and feelings – but it was still good, and was substantial.

There are two ways something can be filled: It can be filled with something bad against the wishes of its owner, or it can be filled with something good in accord with the wishes of its owner. In both cases being "filled" means being endowed with a spiritual quality. When the material in question is good – water, food, people who represent good things, etc. – it means getting the desire for good and the understanding of truth from the Lord. When the material is bad – dust, flies, emotions like despair or terror, etc. – it means being overwhelmed and enslaved by the desire for evil and the false, twisted logic that supports it.

There are a number of references in the Bible to "filling the hand," which has a specific meaning and is dealt with separately.