This is like an advanced floor/ceiling rise effect. When a trigger is activated, the water will rise to a specified height. The water will be submergible at all times (even while it's rising).

Create the submergible water effect (above-water sector and below-water sector connected by S[Channel,7]). Change the height of the above-water sector's floor to the height that you want it to start at. Change the height of the below-water sector's ceiling to the height that you want it to rise to.

Add the following sprites to the above-water sector: S[0,31], A[0,Channel] (Sp[0,Speed]). Make sure the angle of the S[0,31] is facing up. Raise the height of the S[0,31] to the height that you want the water to rise to. If you use an Sp to control the rate of rise, make sure you give the below-water sector an Sp with the same Speed value.

Add the following sprites to the below-water sector: S[0,32], A[0,Channel] (Sp[0,Speed]). Make sure the angle of the S[0,32] is facing down. Raise or lower the S[0,32] to the height that you want the water to start at. If you used an Sp in the above-water sector, make sure you place one in this sector with the same Speed value.

Place either a T[NumberOfActivations,Channel] or else a Switch[ActivationSound,Channel] somewhere in your level to trigger the rising water.

Notes:

• You are going to have to do a bit of math to set the height of both water sector's correctly. If you don't, one sector might keep rising, while the other has already stopped (needless to say, looking totally fake).
• You can also replace the Activator with a Masterswitch, but then the water will only rise once (maybe that's what you want?)
• Use the O key on the below-water sector's walls so they don't rise with the ceiling.