Prophet (SAW)'s Prayers When one sees heavy clouds

Recite:

اللَّهُمَّ إِنَّا نَعُوذُ بِكَ مِنْ شَرِّ مَا أُرْسِلَ بِهِ اللَّهُمَّ صَيِّبَاً نَافِعَاً

"O Allah I seek refuge in You from the evil of what has been sent. O Allah, give us beneficial rain". (Hisnul Hasin)