Without going into Tracy's links deeply, proceed with caution if you are intending to use any of the clear epoxy resins to make your water. Many of them generate sufficient heat to warp a model if mixed and poured too thickly. Go slow, while 1/8 may be too thin - 1/4 may be disasterous. Mix and pour in layers. Color darkly in the bottom layers and make them progressively more transparent in succeding layers. Experiment first before committing your model to an irretrieveable process.
Also, as the resin has a tendency to shrink as it hardens, bases made with the material tend to exhibit the physically impossible trait of showing water climbing up a vertical surface. Are you okay with that? Experiment first.
Some surface ripples may be added using a putty knife/artists pallete knife as the top-most layer approaches hardening. Some model railroaders who have used the stuff have blown on the surface with a heat gun (i.e. a heavy duty hair dryer) to make wind rows as the top layer hardens. The heat gun may be problematical with your model imbedded in the plastic. Did I mention to experiment first?
The recommendations for artists acrylic paints, thinned with clear acrylic gloss varnishes, and topped with a shiny coat of Future floor polish is perhaps the best and most forgiving method to use