As far as I know, this factor is mainly controlled by game shaders.
A while ago TheDarkWraith introduced some changes to waterPS.fx, for addressing the issue of dat unit's keels not showing underwater. His work was released with Dynamic Environment v2.1, under the name of 'Dynamic Environment Shallow Waters'. One side effect of this submod of DynEnv was that it was making the seabottom (and rocks, seaweed, dived submarines, etc) visible through water, especially at shallow depths, hence the name chosen by stoianm.
At a later stage, Pintea suggested some changes to another shader, namely TerrainSurfacePS.fx, for partially obviating the above mentioned flaw. These modifications were released as 'Dynamic Environment Shallow Waters Patch'. The final result was a semi-transparent effect that is nice around mediterranean and tropical shores, but quite unrealistic when applied to harbour's waters.
Too bad, shaders are applied globally, and as far as I know there is no way to limit their effect to certain areas. Parameters that, sure enough, can be set separately for each zone defined in ClimatZones.tga, are the ones found in EnvColors_*.cfg files. They include UnderwaterUpAlpha and UnderwaterDownAlpha, setting
uderwater water transparecy, and a bunch of parameter dealing with sea (underwater and surface) colors.
By making the appropriate changes to the zones around SH5 main harbours in the above mentioned ClimatZones.tga, one can make those areas to feature a darker, greenish (but not lesser transparent) sea surface.
