Hi Stanley
I don´t know if exist a tutorial for it, to apply the Water Effect check my answer here How can I represent water in CityEngine?
Basically all my features were created on ArcGIS then imported on CityEngine. Building Footprints, Streets and Water (just a polygon feature to represent one Lake), everything with Z-value enabled, but you can create polygon on CityEngine, it´s the same process. Here my project (isn´t the final version http://bit.ly/2EbNINM )
In your case, I think will be two river´s features (polygons) Low-Level (ground) and High-Level(Flood) for example.
Feel free to ask-me anytime.