Unlike the quantitative phase of heavy floods, caused by winter rain storms - the flow of Ein-Avdat is weak, but steady. Permanent water drops out from the permeable limestone layered above the impermeable chalk beds.

The complex of Ein-Avdat includes three springs: Ein Ma'ariff, Ein Avdat, and Ein Mor located one above the other. Each of them has a pool, supplied by the stream coming from the higher level. Small side springs contribute small amounts to the main stream, running down and gradually infiltrating into the ground till it disappears. Ein Mor, the lowest pool in the complex, is isolated from the open stream that connects the two other pools, and is filled by ground water running down the surface. Several times in winter, when rain storms happen, a flood washes the canyon, destroys the vegetation and dangers animals and men. But it takes only few hours till it calms down, the stream return to its regular phase, and the Ecosystem starts to restore again.