It is narrated from Sayyidah Aishah (may Allah be pleased with her) that whenever he (peace and blessings be upon him) saw clouds or a wind, he (peace and blessings be upon him) would become alarmed, and when the rain fell he (peace and blessings be upon him) would say: 'Allahumma saqyan nafi'an' (O Allah, make it beneficial rain).
Hadith Referenceالسنن الكبرى للبيهقي / كتاب صلاة الاستسقاء / 6469