The percent is the percent of each color. So if you want the water to be pure red, make every color thats not red 0%.
If you want to make it dark green I suggest either experimenting a little bit with mixing green and a little bit of blue and a low percentage of red. You could always use one of the preset colors if your lazy.
What I suggest doing, since you seem pretty new to this, is picking the Dark Green preset and add a bit of blue to it, then just mess around with it until you have what you want.
Oh, and thank you -Kobas-, i forgot to mention, when your setting water tinting color via Trigger you can also set transparency.