Numbers 20:13

They are the waters of dispute. They are the ones mentioned elsewhere. Pharaoh’s astrologers saw them, [seeing] that the saviour of Israel would be smitten through water. Therefore, they decreed that “every boy who is born must be thrown into the river.”

He was sanctified through them. Since Moshe and Aharon died because of them. When the Holy One, Blessed is He, administers judgment against His holy ones, He is feared and sanctified by mankind. Similarly, it says, “You are awesome, God, from Your sanctuaries.” Similarly, it says, “I am sanctified by those close to Me.”

These are the Waters of Contention, where the sons of Israel contended before the Lord on account of the well that had been hidden; and He was sanctified in them, in Mosheh and Aharon, when (the waters) were given to them.

AND HE WAS SANCTIFIED IN THEM — “in that Moses and Aaron died on account of them [i.e., the waters of Meribah]. When the Holy One, blessed be He, executes judgment upon those who are holy [i.e., near] to Him, He becomes revered and sanctified in people’s eyes, as it is said, In them that are nigh unto Me I will be sanctified, and similarly it is stated, Revered is G-d ‘mimikdashecha’ (out of Thy holy places).” (‘out of Thy holy places’) but mim’kudashecha [‘out of Thy sanctified ones’ — out of those who are holy to His Name, upon whom He executes judgment]” (Rashi, Leviticus 10:3). This is Rashi’s language, and it is also Rabbi Abraham ibn Ezra’s interpretation. But it does not appear to me to be correct, for Moses and Aaron had not yet died and it was not commonly known amongst people that they were to die on account of this sin, so that G-d would become revered as a result of it, as happened with Nadab and Abihu, and at Perez-uzzah. Besides, Scripture states, These are the waters of Meribah, where the children of Israel strove with the Eternal, and He was sanctified ‘by them,’ meaning to say that He was sanctified by those who did the striving [and not through the punishment of Moses and Aaron, as Rashi and Ibn Ezra said], this being related to the expression ‘In them’ that are nigh unto Me I will be sanctified. And according to their explanation [i.e., that of Rashi and Ibn Ezra], it should have said, [These are the waters of Meribah, where the children of Israel strove with the Eternal] “and He became honored in front of them” [the children of Israel].
The correct interpretation appears to me to be that the incident with the first rock took place in the sight of the elders of Israel alone, as it is expressly stated there. But here [in Verse 10] it is said, And Moses and Aaron gathered the assembly together etc. Therefore Scripture states that these waters of Meribah [Strife] which brought about the Divine decree against Moses and Aaron [that they would not enter the Land], were the same waters of Meribah, where the children of Israel strove with the Eternal and He was sanctified in them in the presence of all of them, similar to that which is written, and I shall gather them out of their enemies’ lands, and will be sanctified in them in the sight of many nations.
Know that at the first [incident with the rock] the people quarrelled with Moses — as it is said, And the people strove with Moses, and so also did Moses say, They are almost ready to stone me, Verse 4. — and they [also] tried G-d, saying, Is the Eternal among us, or not?, Verse 7. But here they strove with Him Who is on high, but they did riot test Him. Therefore [Scripture] says that these waters of Meribah [Strife] which were the cause of this decree [against Moses and Aaron] are the same waters of Meribah, where the children of Israel strove with the Eternal, and He was sanctified in them in their presence, and they were not the first [waters of the rock in Horeb], where they tried the Eternal, and He was sanctified only in the sight of the elders of Israel. And since there were two incidents with a rock, Scripture had to explain for which one [of these two events] these righteous men [Moses and Aaron] were punished.

ויקדש בם, G’d’s name had still become sanctified by means of the water which came forth from the rock even though Moses and Aaron had not spoken to the rock.

ויקדש בם, by these very waters G’d did become sanctified later on in the incident which occurred at the river Arnon when He showed these people these unnatural waters as testified to by the Israelites in their song (21,19) ומנחליאל במות that these waters instead of flowing downwards in accordance with the laws of gravity, actually flowed uphill.