Allah tells us that water originates in the sky. This is like the Ayah:

﴿وَأَنزَلْنَا مِنَ السَّمَآءِ مَآءً طَهُوراً﴾

(and We send down pure water from the sky) (25:48). So, Allah sends down water from the sky, and it settles in the earth, then He causes it to flow wherever He wills, and He causes springs, great and small, to flow as needed. Allah says:

﴿فَسَلَكَهُ يَنَابِيعَ فِى الاٌّرْضِ﴾

(and causes it to penetrate the earth, as water springs,) Sa`id bin Jubayr and `Amir Ash-Sha`bi said that all the water on earth has its origins in the sky. Sa`id bin Jubayr said, its origins lie in the snow, meaning that snow piles up in the mountains, then settles at the bottom (of the mountains) and springs flow from the bottom of them.

﴿ثُمَّ يُخْرِجُ بِهِ زَرْعاً مُّخْتَلِفاً أَلْوَانُهُ﴾

(and afterward thereby produces crops of different colors) means, then from the water which comes down from the sky or flows from springs in the earth, He brings forth crops of different colors, i.e., different kinds of forms, tastes, scents, bencfits, etc.

﴿ثُمَّ يَهِـيجُ﴾

(and afterward they wither) means, after they have been ripe and fresh, they become old and you see them turn yellow when they have dried out.

﴿ثُمَّ يَجْعَلُهُ حُطَـماً﴾

(then He makes them dry and broken pieces.) means, then they become brittle.

﴿إِنَّ فِى ذَلِكَ لَذِكْرَى لاٌّوْلِى الاٌّلْبَـبِ﴾

(Verily, in this is a reminder for men of understanding.) means, those who are reminded by this and who learn the lesson from it, that this world is like this -- it is green and fresh and beautiful, then it will become old and ugly. The young man will become a weak, senile old man, and after all of that comes death. The blessed one is the one whose state after death will be good. Allah often likens the life of this world to the way He sends down water from the sky and crops and fruits grow thereby, then they become dry and brittle. This is like the Ayah:

﴿وَاضْرِبْ لَهُم مَّثَلَ الْحَيَوةِ الدُّنْيَا كَمَآءٍ أَنْزَلْنَـهُ مِنَ السَّمَاءِ فَاخْتَلَطَ بِهِ نَبَاتُ الاٌّرْضِ فَأَصْبَحَ هَشِيمًا تَذْرُوهُ الرِّياحُ وَكَانَ اللَّهُ عَلَى كُلِّ شَىْءٍ مُّقْتَدِرًا ﴾

(And put forward to them the example of the life of this world: it is like the water (rain) which We send down from the sky, and the vegetation of the earth mingles with it, and becomes fresh and green. But (later) it becomes dry and broken pieces, which the winds scatter. And Allah is able to do everything) (18:45)