Musannaf Ibn Abi Shayba 21:104

Abu Bakr narrated to us, he said: Abu Usama narrated to us, he said: Ubaydullah narrated to us, from Nafi’, from al-Qasim, who said: When the Messenger of Allah (peace and blessings of Allah be upon him) saw the rain, he would say: "O Allah, make it a beneficial downpour."