Sacamano,
1) The pilot of a 'Mech fallen in L1+ water cannot eject (TO p197), unless the 'Mech has an unbreached full-head ejection system (TO, p310).
2) If the submerged 'Mech has a destroyed Life Support critical hit, the 'Mechwarrior takes one point of damage per turn (TW, p127)
3) If the submerged 'Mech has a working life support, the pilot remains alive until the end of the scenario. What happens then is not covered in the rules.
Given TW play involves 10-second turns, there's no mechanism for resolving the situation during gameplay. After the battle, though, there's plenty of time. Viable suggestions for house-ruling the situation could:
a) The pilot can be rescued by whichever side wins the game.
b) The pilot can take his/her time to try and non-explosively escape from underwater via hatches. Make a PSR, with a +1 target modifier per depth level involved; if successful, the pilot survives.
Example: Jason's Banshee is rammed by a WiGE, and falls from a cliff into depth 3 water. The 'Mech's head is undamaged. As a standard IS pilot, Jason's piloting skill is 5; he must roll 8 (5+3) or better to survive escaping from the depths.