Right, firstly I apologise if this has been posted already.
Look inside (installation location permitting)
C:\Program Files\Ubisoft\Crytek\Far Cry\Levels
There should be a folder for each level. Inside each folder there is a file named level.pak. Open with Winzip or whatever, then look for file named mission_xxx.xml (xxx being the mission name). Search the file for the line named
Water="TerrainWater_OnlySky"
and replace with
Water="TerrainWater"
Save the file, update the zip and now everything should be reflected in the water, including Jack himself, trees, smoke and explosions. I haven't had time to test it yet myself but it sounds good :)
[Edit] Duh!
