Amefurashi

Amefurashi (アメフラシ) is a manga by Atsushi Suzumi. It was first serialized in Monthly Shōnen Sirius in Japan from 2006 to 2007, and was licensed by Del Rey Manga in North America. Kodansha Comics license rescued it, and released both volumes digitally in English.

Plot
Gimmy is just an ordinary teen living in a desert town when his younger twin brother and sister disappear. While searching for them, Gimmy comes face-to-face with a sassy deity, Sora, the rain goddess who provides water to the town. But another goddess, Ciel, wants Sora's sacred tree–so that she can control the rain!