There are lots of ways to make water, you might want to look up how Train set modelers make their waterscapes, one way is a type of "wavey glass" another way is to use stuff called Realistic Water(found at hobby stores in the trainset section). There is a nice How-To Make Realistic Looking Water in the Model Railroader Magazine the July Issue...
Diorama builders would and should look into the techniques used by model railroad builders, it has helped me TREMENDOUSLY, and has gotten me into yet ANOTHER hobby along the same lines as building dioramas and models...