There is not enough detail in your question to give a single answer. I just tried changing the water colour (both as Legacy and an Effect Layer) in build 122411 and it worked.
Are you using the Legacy Water (the old Trainz version of water) which was added using the ground tool in Surveyor (1.0 or Classic)? This is still available in TRS22 using Surveyor Classic but is not recommended. The water colour is set using the Environment Tools - see Water Colour for the details.
Are you using the Water Effect Layer in TRS22 in Surveyor 2.0? This is now the recommended method for adding water. You will need to add a new Effect Layer, give it a name and set its type to Water. You can then set its colour by the three RGB colour values (each from 0.000 to 1.000). Then click the Apply button. Each Water Effect Layer (you can have more than one) covers the entire route and each can have a different colour. There is a learning curve.
