Praise be to Allaah.
Allah, may He be exalted, says (interpretation of the meaning): And He it is Who has created the heavens and the earth in six Days and His Throne was on the water, that He might try you, which of you is the best in deeds [Hood 12:7].
This is a statement by Allah, may He be glorified and exalted, that His Throne was above the water before He created the heavens and earth and what is in them. Qataadah said: Your Lord, may He be blessed and exalted, is telling you how His creation began before He created the heavens and the earth.
Tafseer al-Tabari, 15/246
Al-Bukhaari (2953) narrated from Imraan ibn Husayn (may Allah be pleased with him) that some of the people of Yemen asked the Prophet (blessings and peace of Allah be upon him) this and said: We have come to you to ask you about this matter. He said: There was Allah, and there was nothing else besides Him, and His Throne was over the water. He wrote all things in the Book (in heaven) and He created the heavens and the earth.
Both the verse and the hadeeth are speaking of the beginning of creation, and say that the Throne of Allah, may He be glorified and exalted, was over the water before the creation of heaven and earth.
This does not mean that the Throne is not still over the water.
Al-Bukhaari (6869) and Muslim (1659) narrated that Abu Hurayrah (may Allah be pleased with him) said: The Right Hand of Allaah is full and (its fullness) is not decreased by any spending; it is overflowing by night and day. Think of what He has spent since He created the heavens and the earth, but all this spending had not decreased what is in His Right Hand. He said: And his Throne is over the water, and in His other Hand is the power to bring about death, and He raises some people and brings other low.
Al-Haafiz Ibn Hajar (may Allah have mercy on him) said: In the report of Ishaaq ibn Raahawayh it says and the Throne is over the water. The apparent meaning is that it was like that when the Prophet (blessings and peace of Allah be upon him) spoke these words. The apparent meaning of the hadeeth which comes before it is that the Throne was over the water before the creation of the heavens and earth, and the two hadeeth when taken together indicate that it is still over the water. End quote.
Fath al-Baari, 20/496
The meaning of the word kaana (was) in the verse refers to what happened in the past, before the creation of the heavens and the earth. From his saying in the other hadeeth, His Throne is over the water, it may be understood that it is still like that.
And Allah knows best.