This is an important question that gets asked frequently. I believe based on scripture that he does. In this post I will present the passages that have convinced me of this.
The Omnipotence of God
The power of God is infinite, to deny this is actually a heresy. Just like his power is infinite so to is in knowledge. You can find older posts presenting these doctrines from scripture HERE and HERE. So you can reason fairly simply that God does control the weather for to say he does not would place limits on either his power or his knowledge. Even still though there are clear passages that do positively teach that God controls the weather.
“Also with moisture He loads the thick cloud; He disperses the cloud of His lightning. It changes direction, turning around by His guidance, That it may do whatever He commands it On the face of the inhabited earth. Whether for correction, or for His world, Or for lovingkindness, He causes it to happen.” Job 37:11-13 NASB
“Those who go down to the sea in ships, Who do business on great waters; They have seen the works of the LORD, And His wonders in the deep. For He spoke and raised up a stormy wind, Which lifted up the waves of the sea. They rose up to the heavens, they went down to the depths; Their soul melted away in their misery. They reeled and staggered like a drunken man, And were at their wits’ end. Then they cried to the LORD in their trouble, And He brought them out of their distresses. He caused the storm to be still, So that the waves of the sea were hushed. Then they were glad because they were quiet, So He guided them to their desired haven. Let them give thanks to the LORD for His lovingkindness, And for His wonders to the sons of men!” Psalms 107:28-31 NASB
“”I am the LORD, and there is no other; Besides Me there is no God. I will gird you, though you have not known Me; That men may know from the rising to the setting of the sun That there is no one besides Me. I am the LORD, and there is no other, The One forming light and creating darkness, Causing well-being and creating calamity; I am the LORD who does all these.” Isaiah 45:5-7 NASB
“And He said to them,”Where is your faith?”They were fearful and amazed, saying to one another, “Who then is this, that He commands even the winds and the water, and they obey Him?” Luke 8:25 NASB
The answer is an obvious yes, God does in fact control the weather. To deny this would be to deny the very nature of God, which would be the sin of idolatry.
While it is true that God does in fact control the weather, I would advise against trying to speak on his behalf when he does so. Best case scenario you will probably just be wrong, worst case scenario it would be the sin of using God’s name in vain. Aside from some specific events in the Bible we don’t get a blow by blow detail of God’s reasoning.
The truth is that every city on this planet deserves far greater judgement than any man or woman has ever seen in this life. It is a great mercy that he doesn’t send us all to hell right now. In my opinion, the worst judgement God sends is false teaching. When heresy is allowed to proliferate mans heart is hardened and damned to hell. A storm that calls many to humility and repentance, though tragic, can also be viewed as a mercy in this respect.