I had the same impression about water in TMO. I tried few environmental mods and I recommend that you try Improved Stock Environment v3 - TMO&RFB
http://www.subsim.com/radioroom/showthread.php?t=194657
(as you see this is a mod's version tweaked for TMO)
The mod alone didn't improve look of the water but after installing optional mods, which are
#1 ISE New clouds+Waves
#2 ISE Realistic Colors
it looks very good.
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SH3, GWX 3.0 or NYGM, h.sie/Stiebler hardcoded fixes, patchSH3r, Hitman's GUI, Hide My Sub, Evan82's Uniforms II
SH4 TMO
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