This can be done in many ways, the simplist is to take the standard wad that comes with Gamestudio and assign a water texture to a surface (it moves automatically) creating a water effect. If your looking for realistic looking effects, you need shaders (A6 Commercial or above) to put on a surface, these can do anything from simulating ripples to reflective surfaces. Since you are new I would suggest the previous suggestion.

To tell you the truth I can't remember how to make your own water textures (its 1am over here). So maybe someone else can help you in that catagory.