In this image from 2004 in Afghanistan Kandahar region many small craters are seen. What are they?
These are qanats, a type of antique drainage system common in arid climate regions of the Middle East, particularly in Iran (as mentioned by @Spencer @Winwaed). Some of those are still in use for storage because of lower underground temperature or to access the underground water.
In the picture posted by OP, it further make sense since the underground channels follow linear paths near, around and crossing the small stream, thus providing a remote access to water.
Here is an oblique picture showing the qanats of Bam in Iran (Higher resolution available at the source here).