I starting typing a response to this question because I thought I knew the answer, but now I am not so sure.
I am assuming that you are using the Environment Tools to change the water colour.
Certain Environmental Controls are only saved as part of a Session, not a Route. Others are saved as part of a Route, not a Session. To confuse thing further, some controls (specifically the date) will be saved in either or both, depending on what else you have edited before saving.
Lighting effects, and I am assuming that the water colour is a lighting effect because it is in the same control group, are saved in Session data so you can have different lighting effects in different Sessions (e.g. early morning, late afternoon, night). A Route without a Session will always use the default values for the missing Environmental Controls that would be found in the Session data.
Another way to set the water colour is through the Region Asset, which becomes part of the Route data, not the Session.
