Normally I would suggest tweaking the water via SH3 Commander. If you have a backup copy of your original unaltered game (you should have)....try replacing 'scene DAT file' from: C:\Program Files\Ubisoft\GWXv103\data with the original game version.
Another rule well worth adhering to is, install JSGME and only add anything to tour game via that.
Good Luck
