The continuous water effect is done with a 3D skybox where a camera elsewhere enlarged the water you make beneath it and applies it all around the level edges where the sky is. Problem is water is tricky to get it so it matches the water inside the level and animates at the same time. You have to scale it down 1/16th of it's size since the camera enlarges it 16 times.
For the standing up thing that was done with a point_viewcontrol camera parented to func_doors that give the illusion of getting up and then it is turned off and player control is back on. It's a bit complex but you make the player_start trigger at the mapstart to turn on the camera which follows the func_doors and then ends thus gaining control of the spawn again so place the spawn and trigger where the player should start.
Edit I just re-read it and my reply doesn't make much sense does it >_>...