The transmitted pulse has certain power and can go up to a limited depth usually 200 meters. Beyond this depth, the echoes from the seabed become very weak and the strength is not sufficient to calculate the Doppler shift. In such a case echoes are also available from water layers between 10 and 30 meters below the keel and hence Doppler shift is possible, enabling measurement of speed. But this will give us speed over water.
This is referred to as water track and does not allow for set and drift. The equipment automatically changes over to water track when the echoes from the sea-bed are not strong enough.
When the ship moves at high seas at the usual sea speed it carries some mass of surrounding water with it and thereby providing a distinct layer of water between 10 and 30 meters below the keel and this depth depends on the draft and speed of vessel. Below this depth the water is still and hence there is a distinct separation between the two layers of water which provides the echoing surface of the acoustic waves. These echoes are of course weak since the echoing surface is actually liquid, but stronger than the echoes coming from the depths of over 200 meters. The speed worked out does not depend on the depth from which the echoes are received. The strength of the echoes indicates whether the ship is on bottom track or on water track.