‘A’isha said that when the Prophet (ﷺ) saw something rising in the sky, meaning clouds, he left what he was doing, faced them and said, "O God, I seek refuge in Thee from the evil of what they contain." If God cleared them away he praised Him, and if rain fell he said, "O God, give a beneficial fall.” Abu Dawud, Nasa’i, Ibn Majah and Shafi'i transmitted it, the wording being Shafi'i's.
Source: sunnah.com
Other translations
Arabic
وَعَنْ عَائِشَةَ رَضِيَ اللَّهُ عَنْهَا قَالَتْ: كَانَ النَّبِيُّ صَلَّى اللَّهُ عَلَيْهِ وَسَلَّمَ إِذَا أَبْصَرْنَا شَيْئًا مِنَ السَّمَاءِ تَعْنِي السَّحَابَ تَرَكَ عَمَلَهُ وَاسْتَقْبَلَهُ وَقَالَ: «اللَّهُمَّ إِنِّي أَعُوذُ بِكَ مِنْ شَرِّ مَا فِيهِ» فَإِنْ كَشَفَهُ حَمِدَ الله وَإِن مطرَت قَالَ: «اللَّهُمَّ سَقْيًا نَافِعًا» . رَوَاهُ أَبُو دَاوُدَ وَالنَّسَائِيُّ وَابْنُ مَاجَه وَالشَّافِعِيّ وَاللَّفْظ لَهُ
sunnah.com