Ooh this a tough one Alistair,heres why.
First set your time of day.
next your light angle or Sun position.
Next the color of your water.
Surface tension on the water,so you have to work out what area is sticking out of the water and how the water wraps around it creating tension in the area ripples etc.
Then paint your base colors and use color fills with different blend modes to create contrast giving you the effect of light bleed.
Next is detail clouds and sky etc are what gives water color as its basically color less,so the water color will be a combo of the sky color and the depth of the water and what is in it.
Next is details and caustics.
Hope some of that helps,is not repeat not meant to scare you off though ok 
,stick at it you will get it.
In LOTR they used models and put them in pools of water after they had been incredibly well painted though.After that they used Shake {a high end comping program for ani} and added color and effect etc.
There is a piece on the two towers on the extended version DVD on how they did that piece Alistair.
Heres an airbrushed piece of water I made earlier.
Stu.
