total Warfare p144 for Physical attacks has a section on water.
if the attacker is in..
Depth 1 water: specifically says the mech cannot make charge or death from above attacks.
Depth 2 water: has a list of allowed physicals that does not include death from above.
p149 under Death From Above says you must jump in to the hex, but stop just short. (whatever that means rules wise).
It then says specifically submerged naval vessels cannot be the target of death from above attacks (though why mention that rather than just no submerged unit may be death from aboved?)
Ah, "for purposes of determining LOS, the attacking unit is considered to be in the air above the hex, standing one level higher than the target hex or the level of the hex the attacker occupies, whichever is higher." (wait, isn't that the same hex??) If you are one level above a prone 'mech in level 1 water, the attacker is at level 0, or the surface of the water. And surface units do not have LOS to underwater units (TW p102 Water."This means that units above the water, such as hover or WiGE vehicles, never have LOS to a submerged unit, even if they occupy the same water hex.")
If the target was prone in level 2 water, then the attacker is in level 1 water. Has LOS, but then p144 blocks death from above.