At the time of rain and thunder:

اللَّهُمَّ صَيِّبَاً نَافِعَا‬
Allaahumma Sayyibann Naafi’aa

“O Allaah, (bring) beneficial rain clouds.”
(Bukhari – Fathul-Bari 2/518)

سُبْحَانَ الَّذِي يُسَبِّحُ الرَّعْدُ بِحَمْدِهِ وَالْمَلَائِكَةٌ مِنْ خِيفَتِهِ
SubhanAllaahil ladhii yusabbihur ra’du bi hamdihi wal malaa-ikatu min kheefatihi

“Glory is to Him Whom thunder and angels glorify due to fear of Him.”

[Whenever Abdullaah bin Zubair radhiyaAllaahu anhu would hear thunder, he would abandon all conversation and say this supplication. See al Muwatta 2/992.

May Allah keep us all in His Hifzoamaan. For the rest of it, enjoy the rain! 🙂