This phrase comes from the Torah, specifically from the blessings in the book of Vayikra (Leviticus) 26:4. It is part of the promises Hashem gives to the Jewish people for following His commandments. The blessing of rain "in its season" signifies not just the provision of rain, but rain that falls at the most beneficial and appropriate times, ensuring agricultural prosperity and the well-being of the people.
Rain, in this context, symbolizes not only physical sustenance but also spiritual blessings. When the Jewish people fulfill Hashem's will, they are promised that their physical needs will be met in a timely and abundant manner, which is critical for a society dependent on agriculture. This verse highlights the connection between spiritual observance and material blessing.