For Num 20:13, we have various commentaries (Ellicott, Pulpit, Cambridge Bible) that appear to be agreed that "them" (בָּֽם׃ (bām) - masculine plural) is either:
- The waters of Meribah, in which case the meaning is God was made holy by the miracle of the waters at Meribah, or
- The People, in which case God is made holy in the eyes of the people. Most commentators prefer the latter.
While I agree, there is a common rule (as I have observed) that the Bible writers often employ a clever economy of words by deliberately employing a dual meaning phrase having two meanings when both are intended. I think this is very likely one of them.
If this is true, then God is made holy by the miracle of the waters at Meribah, and this making holy was in the eyes of the people. Thus, both meanings above could be simultaneously intended.