Incorrect! If you have your IOR and Fresnel set, you can have alpha at 1 and you’ll still get transparent renders… don’t believe me, try it out.
Both the glass (IOR 1.53) and the water (1.333) are set as solid as the slider goes. 1.0. it’s the nature of the beast. This is Blender internal, btw. Yafray behaves differently.
The IOR value determines the falloff of incident light. Higher values means that light falls off faster. The effect is quite subtle and changes the distribution function only a little bit. By the examination of many different materials a value of 1.3 to 1.5 have been found fitting. If you know the exact material you are trying to simulate,
You just switch to the cycles renderer and in the materials tab click ‘Use nodes’. ‘Diffuse BSDF’ then becomes a drop-down where you can select different materials. Select glass if you want to use the IOR.