The entire world's water is controlled by worldwc.bgl... the world's waterclass file.
A new waterclass file can be made which will can display custom colors for only the type and area covered. The BGL is quite similar to landclass and can easily be generated with Ground2K, by Christian Fumey.
The trick to customise the water is to use only one waterclass designation... say value #11 ( with #254 transparent for the rest of the colors ), and then pair that waterclass BGL with a new color for #11. That is accomplished by placing the BGL into a local scenery folder, and the texture into a local texture folder.
Normally, you would NOT have a texture folder with either landclass or waterclass, but it is allowed if ALL the texture colors used in the BGL are present in the texture folder.
If you use 5 waterclass values, then you must have the 5 customised textures in the local texture folder.
This will work in FS2004.... it doesn't seem to work in FS2002 or CFS2 ( but it should work? ).
In this way, a river or lake can be colored quite easily. Here's a pic of some water in FS2004... with reflections off so it can be better seen.

Dick